RPS3

Summary: RPS3/uS3 is a canonical structural protein of the human cytosolic small ribosomal subunit.

Reason: This is the core molecular function of RPS3 and is supported by human ribosome structural studies and Falcon's synthesis.

Summary: RPS3 can localize to the nucleus in ribosome-biogenesis trafficking and regulated extra-ribosomal signaling contexts.

Reason: Nuclear localization is supported but is not the primary cellular context of the core ribosomal function.

Summary: RPS3 is a component of the cytosolic small ribosomal subunit.

Reason: This is the core cellular component for RPS3's ribosomal structural function.

Summary: RPS3 has reported pro-apoptotic effects in overexpression/cytokine treatment assays, but this is a context-dependent secondary function.

Reason: The apoptosis evidence is real enough to retain cautiously, but it should not be treated as the core function of this ribosomal protein.

Summary: RPS3 can act as an NF-kB-associated transcriptional specificity factor, but broad RNA polymerase II transcription regulation is not its core function.

Reason: Falcon supports a context-specific NF-kB cofactor/specifier role and cautions against broad generic transcription terms.

Summary: RPS3 binds damaged DNA lesions including AP sites and 8-oxoG, but generic DNA binding is less informative than damaged DNA binding.

Reason: The broad DNA binding term should be replaced by the more specific damaged DNA binding term that is supported by primary binding assays.

Proposed replacements: damaged DNA binding

Summary: RNA binding is plausible for RPS3 through its KH domain, but this is secondary to its ribosomal structural role.

Reason: Falcon supports RNA-binding capacity in a mechanistic/domain context but cautions against overextending it to sequence-specific RNA regulation.

Summary: RPS3/uS3 is a canonical structural protein of the human cytosolic small ribosomal subunit.

Reason: This automated annotation matches the core experimentally supported ribosomal function.

Summary: RPS3 can localize to the nucleus in ribosome-biogenesis trafficking and regulated extra-ribosomal signaling contexts.

Reason: Nuclear localization is supported but secondary to the cytosolic ribosome location of the core function.

Summary: Nucleolar relevance is plausible in ribosome biogenesis, but Falcon found weaker direct evidence for RPS3 protein localization in nucleoli.

Reason: The evidence is more about ribosome biogenesis/gene context than direct RPS3 protein localization to the nucleolus.

Summary: Cytoplasm/cytosol is the expected location for RPS3's core cytosolic ribosomal function.

Reason: The cytoplasmic location is consistent with accepted cytosolic ribosome and translation annotations.

Summary: The automated mitochondrial inner membrane annotation overstates stable, constitutive localization. Direct evidence supports stress-induced RPS3 accumulation in mitochondria, which is represented by separate IDA annotations from PMID:23911537.

Reason: This IEA annotation should not be retained as evidence for stable mitochondrial inner membrane localization. PMID:23911537 supports ROS-induced mitochondrial accumulation for DNA repair, but not constitutive inner membrane residency; the PMID:23911537 IDA mitochondrial annotations should be evaluated separately.

Summary: RPS3 has been reported to localize on the mitotic spindle and act as a microtubule-associated protein during mitosis, so spindle localization has experimental support.

Reason: Spindle localization is supported by direct imaging (PMID:23131551) but is a context-dependent extra-ribosomal/mitotic function rather than the core cytosolic ribosomal location; the more specific mitotic spindle IDA annotation captures it.

Summary: Ribosome localization is core to RPS3's function as a small-subunit ribosomal protein.

Reason: RPS3 is a structural protein of the human cytosolic ribosome.

Summary: RPS3 has secondary evidence for participation in DNA damage processing and base-excision repair contexts.

Reason: DNA repair is supported as an extra-ribosomal function, but Falcon emphasizes that damaged-DNA binding and cofactor-like BER roles are better supported than treating DNA repair as the core function.

Summary: RPS3's core role in the cytosolic ribosome supports translation.

Reason: Translation is the principal biological process associated with RPS3's structural ribosome function.

Summary: RPS3 has been reported to autoregulate its own translation and to be part of translational control mechanisms, but the broad regulation of translation term applied by keyword mapping is loosely supported.

Reason: A specific autoregulatory negative-regulation-of-translation activity is documented (PMID:20217897), so a generic regulation-of-translation term is not wrong but is non-core relative to the structural ribosomal role and is better represented by the specific IDA negative-regulation annotation.

Summary: RPS3 has context-dependent pro-apoptotic evidence from overexpression and cytokine-treatment assays.

Reason: Apoptosis is an extra-ribosomal moonlighting context and should not be treated as the core function.

Summary: RPS3 has reported roles in DNA damage response through damaged-DNA binding and BER-associated interactions.

Reason: This is a secondary extra-ribosomal function and should be interpreted cautiously relative to the core ribosomal role.

Summary: RPS3 is a component of the small ribosomal subunit.

Reason: This cellular component matches the core ribosomal role of RPS3.

Summary: RPS3 has historical AP lyase/endonuclease activity claims, but this broad lyase activity annotation is not the best-supported framing for human RPS3 function.

Reason: The better-supported non-ribosomal activity is damaged-DNA binding and possible BER cofactor activity; intrinsic human AP lyase/endonuclease activity remains secondary and unresolved relative to the core ribosomal role.

Summary: RPS3 is a component of the cytosolic ribosome, specifically the 40S small ribosomal subunit.

Reason: This parent cellular component is consistent with the accepted, more specific cytosolic small ribosomal subunit annotation.

Summary: A keyword-derived generic cell division annotation. RPS3 has reported mitotic-spindle/microtubule functions (PMID:23131551), but the broad cell division term is non-core relative to its ribosomal role and is better represented by the specific spindle assembly/mitotic spindle IMP/IDA annotations.

Reason: RPS3 has documented mitotic roles as a microtubule-associated/spindle protein, so cell division is not wrong, but it is an extra-ribosomal moonlighting context rather than the core function and is captured more specifically by GO:0051225 (spindle assembly) and GO:0072686 (mitotic spindle).

Summary: Direct class I AP endonuclease activity for human RPS3 is historically claimed but remains less secure than damaged-DNA binding and possible BER cofactor activity.

Reason: The annotation likely overstates a debated secondary activity; RPS3's core function is ribosomal, and the stronger DNA repair evidence supports lesion binding/cofactor framing rather than intrinsic class I AP endonuclease activity.

Summary: RPS3 is a constituent of the ribosome, which is a ribonucleoprotein complex; this parent term is consistent with its core ribosomal role.

Reason: As a 40S small-subunit protein, RPS3 is part of a ribonucleoprotein complex (the ribosome). This broad term is correct but is subsumed by the more specific cytosolic small ribosomal subunit annotation.

Summary: RPS3 was identified as a 14-3-3-binding protein in a large-scale proteomic survey of interphase and mitotic 14-3-3 interactors.

Reason: This is a generic protein binding annotation derived from a high-throughput interactome screen. Per curation guidelines protein binding is uninformative, and a single proteomic co-purification does not establish a specific, physiologically core molecular function. Retained as non-core documentation of the interaction.

Summary: This annotation captures RPS3's interaction with RELA (p65) of the NF-kappaB complex. While 'protein binding' is a very general term, the specific interaction with RELA is functionally significant for RPS3's role as a transcription coactivator in NF-kappaB signaling. A more informative annotation would specify the binding partner (RELA).

Reason: The generic 'protein binding' term is too vague. PMID:18045535 specifically demonstrates interaction with RELA/p65 subunit of NF-kappaB. A more appropriate annotation would be to a more specific binding term that captures the functionally relevant interaction with a transcription factor. GO:0140297 (DNA-binding transcription factor binding) or GO:0061629 (RNA polymerase II-specific DNA-binding transcription factor binding) would be more informative.

Proposed replacements: DNA-binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding

Summary: RPS3 was identified as one of a subset of ribosomal proteins targeted by the NEDD8 conjugation pathway in a proteomic/in vivo NEDDylation screen; NEDDylation protects ribosomal proteins from destabilization.

Reason: Generic protein binding from a proteomic NEDDylation screen. This is uninformative as a molecular function (it reflects RPS3 being a NEDD8 substrate rather than a specific binding activity), so it is retained only as non-core documentation of the interaction/modification.

Summary: RPS3 interacts with both p53 and MDM2 through its KH domain and acts as a scaffold on 8-oxoG-containing DNA for binding of MDM2 and p53.

Reason: Generic protein binding term; the specific p53/MDM2 interactions are an extra-ribosomal moonlighting context. Retained as non-core; the more informative MF aspects of this paper are captured by the separate oxidized-pyrimidine DNA binding and negative-regulation-of-ubiquitination annotations from the same reference.

Summary: RPS3 was recovered among 14-3-3-binding proteins in a proteomic survey during C2-ceramide-induced apoptosis.

Reason: Generic protein binding from a high-throughput 14-3-3 affinity proteomics study; uninformative as a specific molecular function and not validated as a physiologically core interaction. Retained as non-core.

Summary: RPS3 was detected as an interactor in a systematic quantitative proteomic study of the cullin-RING ubiquitin ligase (CRL) network.

Reason: Generic protein binding from a large-scale CRL interactome study; uninformative as a specific molecular function and not independently validated for RPS3. Retained as non-core.

Summary: RPS3 was identified among cyclophilin-40 (CyP40)-interacting proteins in a proteomic pull-down survey.

Reason: Generic protein binding from a single-bait interaction proteomics study; uninformative as a specific molecular function and not validated as a physiologically core interaction for RPS3. Retained as non-core.

Summary: In the context of NF-kB signaling, RPS3 nuclear translocation depends on IKKβ-mediated phosphorylation of RPS3 Ser209 and association with the nuclear import machinery (importin-α), as demonstrated by co-IP and functional assays.

Reason: Generic protein binding term. The underlying interactions (IKKβ, importin) are part of RPS3's regulated extra-ribosomal NF-kB role, which is captured more informatively by the NF-kB complex and transcription-regulation annotations. Retained as non-core.

Summary: RPS3 was detected in a bead-based large-scale screen for in vitro kinase substrates.

Reason: Generic protein binding from a high-throughput in vitro kinase-substrate screen; uninformative as a specific molecular function and not validated physiologically. Retained as non-core.

Summary: RPS3 interacts directly with the NF-kB inhibitor IκBα, which sequesters both p65 and RPS3 in the cytoplasm, maintaining an RPS3 pool for the NF-kB pathway.

Reason: Generic protein binding term, but the specific IκBα interaction is part of RPS3's regulated extra-ribosomal NF-kB role. This is non-core relative to the ribosomal function; the NF-kB role is captured by the NF-kB complex and transcription-regulation annotations.

Summary: RPS3 was detected as an interactor in a study centered on LRRK2-mediated phosphorylation of ribosomal protein S15 in Parkinson's disease models.

Reason: Generic protein binding from a study whose focus is RPS15, not RPS3; uninformative as a specific molecular function for RPS3 and not validated as a physiologically core interaction. Retained as non-core.

Summary: RPS3 was identified in a proteomic analysis of chromatin-associated and soluble transcription factor complexes.

Reason: Generic protein binding from a large-scale complex proteomics study; uninformative as a specific molecular function and not independently validated for RPS3. Retained as non-core.

Summary: The caspase-3-generated p65(1-97) fragment interferes with RPS3 and retards its nuclear translocation, dampening RPS3/NF-kB-dependent anti-apoptotic gene expression, supporting a physical RPS3-p65 interaction in NF-kB signaling.

Reason: Generic protein binding term; the specific RPS3-p65 interaction is part of RPS3's extra-ribosomal NF-kB specifier role, captured more informatively by the NF-kB complex and transcription-regulation annotations. Retained as non-core.

Summary: RPS3 was detected among histone-interacting proteins by crosslinking mass spectrometry in intact cell nuclei.

Reason: Generic protein binding from a high-throughput crosslinking-MS histone interactome study; uninformative as a specific molecular function and not independently validated for RPS3. Retained as non-core.

Summary: RPS3 was detected as an interactor in a study of LRRK2-G2019S regulation of SERCA activity and ER stress in astrocytes.

Reason: Generic protein binding from a study not focused on RPS3; uninformative as a specific molecular function for RPS3 and not validated as a physiologically core interaction. Retained as non-core.

Summary: RPS3 appears in the HuRI reference map of the human binary protein interactome (yeast two-hybrid).

Reason: Generic protein binding from a genome-scale binary interactome map; uninformative as a specific molecular function and not individually validated for RPS3. Retained as non-core.

Summary: RPS3 was detected in an interactome map of neurodegenerative disease proteins.

Reason: Generic protein binding from a large-scale neurodegenerative-disease interactome study; uninformative as a specific molecular function and not independently validated for RPS3. Retained as non-core.

Summary: RPS3 appears in the BioPlex dual proteome-scale AP-MS interaction networks.

Reason: Generic protein binding from a genome-scale AP-MS interactome; for an abundant ribosomal protein such co-purifications are expected and uninformative as a specific molecular function. Retained as non-core.

Summary: RPS3 was characterized in the OpenCell endogenous-tagging interaction/ localization atlas of human cellular organization.

Reason: Generic protein binding from a systematic endogenous-tagging interactome atlas; uninformative as a specific molecular function. Retained as non-core.

Summary: RPS3 was identified in a systematic study of post-transcriptional regulatory modules.

Reason: Generic protein binding from a high-throughput post-transcriptional regulatory network study; uninformative as a specific molecular function and not independently validated for RPS3. Retained as non-core.

Summary: RPS3 was included in multimodal cell maps integrating imaging and AP-MS data for structural and functional genomics.

Reason: Generic protein binding from a large-scale multimodal interactome/imaging study; uninformative as a specific molecular function. Retained as non-core.

Summary: RPS3 has historical AP-site endonuclease activity claims, but intrinsic human AP endonuclease activity is not as well supported as damaged-DNA binding and possible BER cofactor activity.

Reason: This automated AP-site endonuclease annotation likely overstates a debated secondary activity. The current synthesis supports lesion binding and BER-associated cofactor roles more strongly than intrinsic human AP-site endonuclease activity.

Summary: RPS3 is a component of the cytosolic small ribosomal subunit (40S).

Reason: This automated orthology-based annotation matches the core ribosomal cellular component, consistent with the accepted IBA/IDA cytosolic small ribosomal subunit annotations.

Summary: RPS3 appears in synapse/postsynaptic density proteomic datasets and is used as a ribosome marker in synaptic compartments, but this most likely reflects local translation machinery near synapses rather than a stable, RPS3-specific synaptic component.

Reason: The synapse localization is an orthology-transferred annotation based on ribosome/translation-machinery presence in synaptic compartments. Per the deep-research synthesis, evidence is indirect for RPS3-specific synaptic residency, so this is better treated as an over-annotation relative to the core cytosolic ribosome location.

Summary: This annotation is an over-annotation. PMID:18045535 demonstrates that RPS3 acts as a non-Rel subunit of NF-kappaB complexes that synergistically enhances DNA binding of p65 homodimer and p65-p50 heterodimer complexes. RPS3 contains a KH domain (an RNA-binding domain, not a DNA-binding transcription factor domain) and interacts with the NF-kappaB complex via protein-protein interactions with RELA/p65. The study shows RPS3 forms part of the NF-kappaB complex bound to regulatory DNA sites, but RPS3 itself does not directly bind DNA with sequence specificity. This is transcription coactivator activity, not DNA-binding transcription factor activity. The term GO:0001228 requires intrinsic sequence-specific DNA binding, which RPS3 lacks.

Reason: The annotation to GO:0001228 (DNA-binding transcription activator activity, RNA polymerase II-specific) is incorrect because this term requires the protein to directly bind DNA in a sequence-specific manner to modulate transcription. RPS3 does not possess a canonical DNA-binding domain for transcriptional regulation - its KH domain is an RNA-binding motif. Per PMID:18045535, RPS3 functions as "a non-Rel subunit of p65 homodimer and p65-p50 heterodimer DNA-binding complexes that synergistically enhances DNA binding." RPS3 acts through protein-protein interactions with the NF-kappaB transcription factors, enhancing their activity. This is the definition of transcription coactivator activity (GO:0003713), not DNA-binding transcription factor activity. The appropriate replacement annotation is GO:0003713 (transcription coactivator activity); DNA-binding transcription factor binding is captured by a separate accepted GO:0140297 annotation.

Proposed replacements: transcription coactivator activity

Summary: An immunofluorescence-based ER annotation. Ribosomes engaged in co-translational translocation associate with the rough ER, but there is no direct RPS3-specific evidence supporting stable ER residency as a distinct function.

Reason: ER signal for a ribosomal protein most plausibly reflects ER-associated (rough ER) ribosomes rather than an RPS3-specific ER localization. The deep-research synthesis found no direct RPS3-specific support for stable ER localization, so this is treated as an over-annotation relative to the core cytosolic ribosome location.

Summary: RPS3 localizes to the cytosol as part of the cytosolic ribosome.

Reason: Cytosol is the expected cellular location for RPS3's core cytosolic ribosomal function and is consistent with the accepted cytosolic ribosome annotation.

Summary: RPS3 is a 40S small-subunit protein of the human cytosolic ribosome and thereby participates in cytoplasmic translation.

Reason: Cytoplasmic translation is the core biological process for RPS3's structural ribosomal role, supported by the near-atomic structure of the human 80S ribosome.

Summary: RPS3 is located in the cytoplasm as part of the cytosolic ribosome.

Reason: Cytoplasm is the expected, core cellular location for RPS3's cytosolic ribosomal function, consistent with the human 80S ribosome structure and accepted cytosol/cytosolic ribosome annotations.

Summary: RPS3 was cloned as the human S3 ribosomal protein, a component of the translation machinery, overexpressed in colorectal cancer.

Reason: Cytoplasmic translation is the core process for this small-subunit ribosomal protein. The reference establishes RPS3 as the human S3 ribosomal protein.

Summary: RPS3 was identified by protein sequencing and mass spectrometry as one of the proteins of the human 40S ribosomal subunit, supporting its role in cytoplasmic translation.

Reason: Cytoplasmic translation is the core process inferred from RPS3's experimentally confirmed identity as a 40S small-subunit ribosomal protein.

Summary: RPS3 is a 40S small-subunit protein located at the mRNA entry channel and is part of the 40S complex recruited during cap-independent (HCV IRES) and canonical translation initiation.

Reason: RPS3 sits at the mRNA entry channel of the 40S subunit and contacts mRNA in initiation complexes (PMID:18464793), so participation in cytoplasmic translational initiation is consistent with its core ribosomal role. The reference identifies RPS3 as part of native and IRES-bound 40S complexes.

Summary: This annotation reflects RPS3's role in enhancing NF-kappaB-mediated transcription as demonstrated in PMID:18045535. The study showed that RPS3 knockdown impaired NF-kappaB-mediated transcription of selected p65 target genes, and lymphocyte-activating stimuli caused nuclear translocation of RPS3 to form part of NF-kappaB bound to specific regulatory sites in chromatin. While this is a biological process annotation that could be retained, it should be noted that RPS3's effect on transcription is indirect - through its role as a coactivator of NF-kappaB rather than as a direct transcription factor.

Reason: The biological process annotation to positive regulation of DNA-templated transcription initiation is appropriate because RPS3 does positively regulate transcription through its role in the NF-kappaB complex, even though this regulation is through protein-protein interactions rather than direct DNA binding. PMID:18045535 demonstrates that RPS3 is "an essential but previously unknown subunit of NF-kappaB involved in the regulation of key genes in rapid cellular activation responses."

Summary: RPS3 was detected in a proteomic characterization of the isolated human postsynaptic density, consistent with ribosome/local-translation machinery at synapses.

Reason: Detection in an isolated PSD proteome most likely reflects synaptic ribosomes/local translation machinery rather than an RPS3-specific structural role at the postsynaptic density. Retained as non-core given the indirect, proteome-survey nature of the evidence.

Summary: Duplicate (IDA) of the postsynaptic density detection from the same human PSD proteome study.

Reason: Same rationale as the EXP-coded postsynaptic density annotation from this reference: most likely reflects synaptic ribosomes/local translation machinery rather than an RPS3-specific PSD structural role. Retained as non-core.

Summary: RPS3 is a component of the cytosolic ribosome, specifically the 40S small ribosomal subunit.

Reason: This cellular component is supported by structural evidence for the human cytosolic 80S ribosome and is consistent with the accepted cytosolic small ribosomal subunit annotation.

Summary: Human RPS3 binds damaged DNA, including abasic (AP) sites and 8-oxoG lesions, with high apparent affinity as shown by surface plasmon resonance.

Reason: Damaged DNA binding is a well-supported extra-ribosomal molecular function of human RPS3 (multiple independent IDA assays: PMID:14706345, PMID:18610840, PMID:16737853). It is a genuine moonlighting activity but secondary to the core ribosomal structural function, so retained as non-core.

Summary: Human RPS3 physically interacts with the BER enzymes OGG1 and APE1/Ref-1 and can stimulate OGG1 N-glycosylase activity, supporting participation in base-excision repair as a binding partner/modulator rather than as a core BER enzyme.

Reason: RPS3 participates in BER through cofactor-like interactions (binding and stimulating OGG1/APE1; PMID:18973764 shows it also stimulates UNG), but this is an extra-ribosomal moonlighting role; note that under some conditions bound RPS3 can inhibit OGG1 repair (PMID:16737853), so the role is context-dependent. Retained as non-core.

Summary: RPS3 is phosphorylated by PKCdelta, which interacts with RPS3 and mobilizes non-ribosomal RPS3 to the nucleus for DNA repair.

Reason: Generic protein binding term; the specific PKCdelta interaction is part of the regulated extra-ribosomal DNA-repair switch and is non-core relative to the ribosomal function. Retained as non-core documentation.

Summary: RPS3 knockdown increased sensitivity to genotoxic stress, and the phosphorylation-dependent repair endonuclease activity of non-ribosomal RPS3 was required for this protection, supporting an extra-ribosomal DNA repair role.

Reason: DNA repair is a documented extra-ribosomal moonlighting function but is secondary to the core ribosomal role. Note that other work reports RPS3 knockdown protects cells from genotoxic stress (PMID:17049931), so the net effect on repair is context-dependent.

Summary: RPS3 depletion caused mitotic arrest at metaphase with abnormal spindle shape and chromosome movement, consistent with a role in proper chromosome segregation via its mitotic-spindle/microtubule function.

Reason: The chromosome segregation phenotype is downstream of RPS3's reported microtubule-associated/spindle role during mitosis, an extra-ribosomal moonlighting context rather than the core ribosomal function. Retained as non-core.

Summary: RPS3 up-regulated the proapoptotic proteins Dp5/Hrk and Bim by binding to and acting synergistically with the transcription factor E2F1 in neuronal apoptosis.

Reason: This positive regulation of gene expression is an extra-ribosomal transcriptional-coregulator activity (via E2F1), context-specific to neuronal apoptosis, and non-core relative to the ribosomal role. The mechanistic E2F1 interaction is captured by the DNA-binding transcription factor binding annotation from the same reference.

Summary: Under elevated ROS, RPS3 accumulates in the mitochondria (entry mediated by HSP90/HSP70/TOM70) to participate in mtDNA damage repair.

Reason: This IDA captures stress-induced (ROS-triggered) mitochondrial accumulation of RPS3 for mtDNA damage surveillance, a regulated extra-ribosomal context, not constitutive inner-membrane residency. It is kept as non-core, distinct from the broad IEA mitochondrial inner membrane annotation that was removed.

Summary: RPS3 accumulates within mitochondria under oxidative stress to repair mitochondrial DNA, consistent with localization to the mitochondrial matrix where the mtDNA resides.

Reason: Stress-induced mitochondrial localization for mtDNA repair is a regulated extra-ribosomal moonlighting role, secondary to the core cytosolic ribosomal function. Retained as non-core.

Summary: RPS3 physically interacts with TRADD and is recruited to the death-inducing signaling complex (DISC) to promote caspase-dependent JNK activation and apoptosis under stress.

Reason: Generic protein binding term; the specific TRADD interaction underlies an extra-ribosomal pro-apoptotic moonlighting role and is non-core relative to the ribosomal function. Retained as non-core.

Summary: The enterohemorrhagic E. coli type III secretion effectors NleH1/NleH2 bind the N-terminus of human RPS3 to subvert RPS3-dependent NF-kB function.

Reason: Generic protein binding term capturing a host-pathogen interaction relevant to RPS3's NF-kB role; non-core relative to the ribosomal function. Retained as non-core.

Summary: Well-supported annotation. PMID:20605787 demonstrates that RPS3 binds to the E2F1 transcription factor and acts synergistically with E2F1 to up-regulate proapoptotic proteins Dp5/Hrk and Bim. This interaction is regulated by Akt-mediated phosphorylation of RPS3, which perturbs its interaction with E2F1. This annotation is appropriate and supports the role of RPS3 as a transcriptional coregulator that binds transcription factors rather than DNA directly.

Reason: The annotation to DNA-binding transcription factor binding is correct based on the evidence in PMID:20605787 showing RPS3 physically interacts with E2F1, a DNA-binding transcription factor. This is consistent with RPS3's role as a transcriptional coregulator that modulates transcription through protein-protein interactions with transcription factors (both E2F1 and NF-kappaB/RELA).

Summary: RPS3 is part of the human 80S ribosome resolved by cryo-EM, supporting its role in cytoplasmic translation.

Reason: Cytoplasmic translation is the core biological process for RPS3, inferred from its experimentally confirmed structural presence in the human cytosolic ribosome.

Summary: RPS3/uS3 is resolved as a structural protein of the human cytosolic small ribosomal subunit in the 80S ribosome cryo-EM structure.

Reason: This is the core, directly-evidenced molecular function of RPS3.

Summary: RPS3 interacts with HSP70 (with HSP90 and TOM70) to regulate its entry into mitochondria during oxidative stress.

Reason: This is a specific, directly-evidenced chaperone interaction supporting RPS3's stress-induced mitochondrial trafficking, an extra-ribosomal moonlighting context. More informative than generic protein binding, but non-core relative to the ribosomal function.

Summary: Elevated cellular ROS triggers RPS3 accumulation in mitochondria for mtDNA repair and a decrease in protein synthesis, indicating a cellular response to reactive oxygen species.

Reason: RPS3's ROS-responsive mitochondrial relocalization is a regulated extra-ribosomal stress response, non-core relative to its ribosomal function. Retained as non-core.

Summary: Human RPS3 interacts with uracil-DNA glycosylase (UNG) and stimulates its glycosylase activity, as shown by co-IP and GST pull-down assays.

Reason: Enzyme binding here captures a specific, directly-evidenced interaction with a BER enzyme (UNG); more informative than generic protein binding but part of RPS3's extra-ribosomal BER-cofactor moonlighting role, so non-core.

Summary: Study of ZNF598-mediated site-specific 40S ribosomal ubiquitination initiating ribosome-associated quality control; RPS3/uS3 is a 40S component in this context.

Reason: Generic protein binding term arising from a ribosome-associated quality control study; for an abundant 40S protein this association is expected and uninformative as a specific molecular function. Retained as non-core.

Summary: ZNF598 and RACK1 regulate 40S ribosomal ubiquitylation during ribosome-associated quality control; RACK1 regulates ubiquitination of RPS2, RPS3, and RPS20.

Reason: Generic protein binding term from a ribosome-associated quality control study. The specific finding (RACK1-regulated RPS3 ubiquitylation) is part of ribosome regulation rather than a discrete RPS3 binding function; retained as non-core.

Summary: Following genotoxic stress, human RPS3 translocates from the cytoplasm to the nucleus (dependent on ERK-mediated T42 phosphorylation), where it co-localizes with 8-oxoG damage foci.

Reason: Stimulus-dependent nuclear translocation is well documented but represents a regulated extra-ribosomal DNA-damage-response context rather than the core cytosolic ribosomal location. Retained as non-core.

Summary: Nuclear localization of RPS3 in response to activating stimuli requires IKKβ-mediated phosphorylation of RPS3 Ser209, as shown using phospho-mutant analysis.

Reason: Regulated, stimulus-dependent nuclear localization tied to NF-kB signaling; non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 was detected in a high-throughput proteomic analysis of isolated focal adhesions.

Reason: Detection of an abundant ribosomal protein in a focal-adhesion proteome is most plausibly a co-isolation/contaminant signal rather than evidence of an RPS3-specific focal adhesion role. No targeted validation supports stable focal-adhesion localization, so this is treated as an over-annotation.

Summary: Well-supported annotation. PMID:18045535 used tandem affinity purification and mass spectrometry to identify RPS3 as a component of the NF-kappaB complex. The study clearly shows that RPS3 is "a non-Rel subunit of p65 homodimer and p65-p50 heterodimer DNA-binding complexes." RPS3 interacts with RELA (p65) and forms part of the NF-kappaB transcription factor complex bound to chromatin in response to activating stimuli.

Reason: The proteomic approach in PMID:18045535 directly demonstrates RPS3 is a component of NF-kappaB complexes. This was validated by co-IP experiments and functional studies showing RPS3 is essential for NF-kappaB function in gene regulation.

Summary: RPS3 is present in the cytosol, where it associates with NF-kB inhibitory complexes prior to stimulus-induced nuclear translocation.

Reason: Cytosol is the expected, core cellular location for RPS3 (cytosolic ribosome), consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: RPS3 stimulates the uracil-excision (glycosylase) activity of UNG and its knockdown reduces uracil-excision activity in cell extracts, supporting positive regulation of base-excision repair.

Reason: RPS3 positively regulates BER as a cofactor that stimulates UNG (and OGG1, PMID:15518571) rather than acting as a core BER enzyme. This is a genuine extra-ribosomal moonlighting role, retained as non-core. Note that under conditions where RPS3 binds 8-oxoG it can instead inhibit OGG1 repair (PMID:16737853), so the regulation is context-dependent.

Summary: RPS3 was identified among ribosomal proteins/ribonucleoproteins that co-purify with the pestivirus N-terminal protease Npro in the ribonucleoprotein complex.

Reason: Generic protein binding from a viral-protein interaction proteomics study; for an abundant ribosomal protein this co-purification is expected and uninformative as a specific molecular function. Retained as non-core.

Summary: Free (non-ribosomal) RPS3 binds its own cognate mRNA via its C-terminal domain and represses its own translation in a feedback mechanism.

Reason: This is a specific, directly-evidenced autoregulatory negative regulation of translation. It is a genuine but specialized function distinct from the core structural ribosomal role, so retained as non-core.

Summary: RPS3 participates in NF-kB-dependent transcriptional responses; in this study its nuclear abundance and RPS3/NF-kB-dependent reporter activity are modulated, and RPS3 functions within TNF/NF-kB activation pathways.

Reason: This term reflects RPS3's extra-ribosomal participation in NF-kB-mediated cytokine responses, a context-dependent moonlighting role rather than the core ribosomal function. Retained as non-core.

Summary: RPS3 has a nuclear pool whose abundance is modulated during NF-kB signaling (NleH1 reduced the nuclear abundance of RPS3).

Reason: Nuclear localization in the NF-kB context is a regulated extra-ribosomal pool, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 acts as a specifier subunit that positively contributes to NF-kB-dependent transcription; bacterial effector binding to RPS3 subverts this NF-kB function.

Reason: RPS3's positive contribution to NF-kB-dependent transcription is a well-supported extra-ribosomal moonlighting role. The specific "non-canonical" qualifier is not strongly distinguished in this reference (which centers on RPS3/p65 transcriptional complexes), but the broad positive NF-kB regulation is supported; retained as non-core.

Summary: RPS3's mitochondrial entry under oxidative stress is regulated by interaction with HSP90, HSP70, and TOM70.

Reason: Generic protein binding term from the mitochondrial mtDNA-surveillance study; the specific chaperone/TOM70 interactions are captured more informatively by the Hsp70/Hsp90 binding annotations from the same reference. Retained as non-core.

Summary: Increasing mitochondrial RPS3 levels reduced cellular ROS and rescued mtDNA damage, indicating RPS3 positively contributes to repair of damaged mitochondrial DNA under oxidative stress.

Reason: Positive regulation of (mitochondrial) DNA repair is a stress-induced extra-ribosomal moonlighting role, non-core relative to the ribosomal function. Retained as non-core.

Summary: RPS3 interacts with HSP90 in the cytosol; geldanamycin disruption of this interaction stimulates RPS3 accumulation in mitochondria.

Reason: Specific, directly-evidenced HSP90 interaction governing RPS3's stress-induced mitochondrial trafficking; more informative than generic protein binding but part of an extra-ribosomal context, so non-core.

Summary: RPS3 relocalizes to mitochondria in response to oxidative (ROS/H2O2) stress to participate in mtDNA damage surveillance.

Reason: Specific oxidative-stress (hydrogen peroxide) response captured by RPS3's stress-induced mitochondrial trafficking, an extra-ribosomal role; non-core relative to the ribosomal function. Retained as non-core.

Summary: During stress-induced apoptosis, GFP-RPS3 co-localized with TRADD around the plasma membrane (and in the cytoplasm) at the death-inducing signaling complex.

Reason: Plasma-membrane-proximal localization is a transient, apoptosis-context observation tied to DISC recruitment, not a stable RPS3 plasma membrane residency. Retained as non-core given the specialized, context-dependent nature.

Summary: RPS3 localizes on the mitotic spindle and functions as a microtubule-associated protein, with its depletion decreasing microtubule polymerization.

Reason: Microtubule binding supports a directly-evidenced mitotic microtubule-associated-protein moonlighting role, distinct from and secondary to the core ribosomal function. Retained as non-core.

Summary: RPS3 associates with the mitotic spindle and microtubules as a microtubule-associated protein.

Reason: Tubulin/microtubule binding supports RPS3's directly-evidenced mitotic MAP role, an extra-ribosomal moonlighting function secondary to the core ribosomal role. Retained as non-core.

Summary: RPS3 depletion decreased microtubule polymerization, indicating RPS3 promotes microtubule polymerization during mitosis.

Reason: Directly supported by loss-of-function evidence, but part of RPS3's mitotic microtubule moonlighting role rather than the core ribosomal function. Retained as non-core.

Summary: RPS3 depletion produced abnormal spindle shape and mitotic arrest, consistent with a role in proper spindle assembly.

Reason: Spindle assembly is supported by loss-of-function data but reflects RPS3's mitotic microtubule moonlighting role, secondary to the core ribosomal function. Retained as non-core.

Summary: RPS3 specifically localizes on the mitotic spindle during mitosis as shown by direct imaging.

Reason: Direct imaging supports mitotic spindle localization, an extra-ribosomal moonlighting context distinct from and secondary to the cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 sensitizes genotoxic (DNA-damage) stress-induced apoptosis by activating JNK in a caspase-dependent manner through interaction with TRADD at the DISC.

Reason: RPS3's pro-apoptotic activity in response to genotoxic stress is an extra-ribosomal moonlighting role demonstrated by overexpression/interaction experiments, secondary to the core ribosomal function. Retained as non-core.

Summary: Free RPS3 binds RNA, including its own cognate mRNA and 18S rRNA, via its C-terminal domain (independent of the KH domain).

Reason: RNA binding is a directly-evidenced activity consistent with RPS3's KH domain and its rRNA contacts in the ribosome, and underlies its translational autoregulation. It is secondary to the core structural ribosomal role; retained as non-core.

Summary: Nuclear-accumulated RPS3 is reported to function as an endonuclease, contributing to DNA repair activity in neuronal cells.

Reason: DNA endonuclease activity reflects RPS3's historically reported AP/base-damage endonuclease moonlighting activity. The intrinsic catalytic status of human RPS3 remains debated (PMID:18610840 finds only AP-site beta-elimination and questions in vivo relevance), so this is retained as a non-core, context-dependent activity rather than a core function.

Summary: Cdk1-mediated phosphorylation of RPS3 at Thr221 during G2/M promotes its nuclear accumulation.

Reason: Regulated, cell-cycle-dependent nuclear accumulation is an extra-ribosomal context, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: A pool of free RPS3 exists in the cytoplasm (outside ribosomes), where it binds its own mRNA to autoregulate translation.

Reason: Cytoplasm is the expected, core location for RPS3 (cytosolic ribosome and free cytoplasmic pool), consistent with accepted cytosol/cytoplasm annotations.

Summary: RPS3 is present in the cytoplasm, with a phosphorylation-regulated shift to nuclear accumulation during G2/M.

Reason: Cytoplasm is the expected, core cellular location for RPS3, consistent with its cytosolic ribosomal function.

Summary: Most of the cellular RPS3 pool is located in the ribosome, consistent with its core role as a ribosomal protein.

Reason: Ribosome localization is core to RPS3's function as a 40S small-subunit protein.

Summary: RPS3 is a physiological target of Akt kinase; NGF-stimulated Akt phosphorylates RPS3 at Thr70, and this phosphorylation is required for Akt binding to RPS3.

Reason: Kinase binding captures the directly-evidenced Akt interaction that regulates RPS3's pro-apoptotic/DNA-repair switch, an extra-ribosomal regulatory context. More informative than generic protein binding but non-core relative to the ribosomal role.

Summary: RPS3 interacts with the cell-cycle kinase Cdk1, which phosphorylates it during G2/M phase, as shown by co-IP and GST pull-down.

Reason: Protein kinase binding captures the directly-evidenced Cdk1 interaction that regulates RPS3's mitotic phosphorylation/nuclear accumulation, an extra-ribosomal regulatory context. More informative than generic protein binding but non-core.

Summary: RPS3 acts as an Akt-regulated molecular switch in neuronal apoptosis; abolishing Akt-mediated phosphorylation accelerated apoptotic cell death, while RPS3 induced apoptosis via E2F1-dependent gene up-regulation.

Reason: Regulation of apoptosis is a context-dependent extra-ribosomal moonlighting role of RPS3, secondary to the core ribosomal function. Retained as non-core.

Summary: RPS3 interacts with SUMO-1 (identified by yeast two-hybrid) and is sumoylated, which increases its protein stability.

Reason: This captures a specific interaction with the SUMO modification machinery that regulates RPS3 stability, an extra-ribosomal regulatory context. Retained as non-core. [Note: the interactor identified is SUMO-1 itself; the "conjugating enzyme binding" framing is a curation interpretation of the SUMO-pathway interaction.]

Summary: Reactome places RPS3 in the nucleoplasm in the context of pre-40S particle processing during ribosome biogenesis (pre-rRNA processing en route from nucleus to cytosol).

Reason: Nucleoplasmic localization reflects the transient nuclear phase of ribosome biogenesis/pre-40S trafficking, not the mature cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 interacts with MDM2 and p53; under oxidative stress, RPS3 knockdown led to loss of the MDM2 E3 ubiquitin ligase domain and decreased p53, implicating RPS3 in regulating MDM2-mediated ubiquitination of p53.

Reason: This is an extra-ribosomal moonlighting role in the p53/MDM2 axis. The evidence is indirect (effects on MDM2/p53 levels under stress) rather than a direct ubiquitination assay, and is secondary to the core ribosomal function. Retained as non-core.

Summary: RPS3 binds an 8-oxoG-containing duplex oligonucleotide and acts as a scaffold for binding of MDM2 and p53 at the damaged DNA.

Reason: Damaged/oxidized DNA binding by RPS3 is well-supported (PMID:14706345, PMID:18610840), and DNA-pull-down here shows binding to an 8-oxoG duplex. This is an extra-ribosomal moonlighting activity, secondary to the core ribosomal function. [The 8-oxoG lesion is an oxidized purine; the term used is oxidized pyrimidine DNA binding, a minor mismatch, but binding to oxidatively damaged DNA is supported.]

Summary: Phosphorylation of non-ribosomal RPS3 by PKCdelta increased its repair (AP/damage) endonuclease activity.

Reason: AP-site endonuclease activity is a historically reported moonlighting activity of RPS3. Its intrinsic catalytic relevance in human cells remains debated (PMID:18610840 finds only AP-site beta-elimination and questions global in vivo repair), so this is retained as a non-core, context-dependent activity rather than a core function.

Summary: PKCdelta phosphorylation mobilizes non-ribosomal RPS3 to the nucleus to repair damaged DNA.

Reason: Stimulus/phosphorylation-dependent nuclear localization is a regulated extra-ribosomal context, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 is present in the cytoplasm, with a phosphorylation-regulated non-ribosomal pool that relocates to the nucleus upon DNA damage.

Reason: Cytoplasm is the expected, core cellular location for RPS3, consistent with its cytosolic ribosomal function.

Summary: RPS3 is a component of the 40S ribosomal subunit involved in translation.

Reason: Ribosome localization is core to RPS3's role as a small-subunit ribosomal protein.

Summary: Recombinant human RPS3 binds DNA, including undamaged DNA; in this study binding to undamaged DNA was actually more efficient than to several damaged lesions.

Reason: Generic DNA binding is less informative than the specific damaged-DNA binding activity that is the functionally relevant moonlighting feature of RPS3; the same reference also documents damaged DNA binding. Recommend the more specific damaged DNA binding term (also separately annotated from this reference).

Proposed replacements: damaged DNA binding

Summary: Recombinant human RPS3 binds and cleaves AP-site-containing DNA substrates (via beta-elimination), confirming damaged-DNA binding.

Reason: Damaged DNA binding is a well-supported extra-ribosomal activity, secondary to the core ribosomal function. Retained as non-core.

Summary: Recombinant human RPS3 cleaves AP sites via a beta-elimination (AP lyase) mechanism but does not cleave substrates containing other lesions, and the authors question its in vivo global repair relevance.

Reason: AP-site cleavage activity is supported in vitro but is mechanistically an AP lyase (beta-elimination) and its physiological/global in vivo relevance is doubted by the authors. It is a context-dependent moonlighting activity, secondary to the core ribosomal function; retained as non-core.

Summary: Arginine methylation of RPS3 by PRMT1 is required for its import into the nucleus/nucleolus and subsequent incorporation into the ribosome.

Reason: Nuclear/nucleolar localization here reflects the ribosome-biogenesis trafficking phase, not the mature cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 is imported into the nucleolus (dependent on PRMT1 arginine methylation) for small-subunit ribosome assembly.

Reason: Nucleolar localization reflects the ribosome-biogenesis/assembly phase of RPS3, distinct from the mature cytosolic ribosomal location. This is a direct functional study (unlike the weaker IEA nucleolus annotation that was marked over-annotated), so retained as non-core.

Summary: RPS3 is incorporated into the ribosome (40S small subunit), a process that depends on its PRMT1-mediated arginine methylation.

Reason: Ribosome localization/incorporation is core to RPS3's function as a 40S small-subunit ribosomal protein.

Summary: Recombinant human RPS3 cleaved AP sites by beta-elimination but did NOT cleave substrates containing oxidized/deaminated bases (8-oxoguanine, uracil, hypoxanthine, etc.), so it lacks DNA glycosylase activity.

Reason: The NOT annotation is well-supported: despite sequence-based predictions, RPS3 has no detectable DNA N-glycosylase activity. Accept the negation as correctly representing the experimental result.

Summary: RPS3 is methylated by and interacts with protein arginine methyltransferase 1 (PRMT1), which regulates its nucleolar import and ribosome assembly.

Reason: Enzyme binding here captures the directly-evidenced PRMT1 interaction that governs RPS3 modification and ribosome assembly. More informative than generic protein binding; it relates to ribosome biogenesis regulation but is retained as non-core relative to the structural ribosomal function.

Summary: RPS3 interacts with 18S rRNA, the rRNA of the small (40S) ribosomal subunit, consistent with its structural role in the small subunit.

Reason: Small-subunit rRNA binding is consistent with RPS3's core structural role in the 40S subunit, where it contacts 18S rRNA. The 18S rRNA interaction is directly documented (PMID:20217897), supporting this MF as core.

Summary: Mammalian RPS3 nicks DNA containing AP sites and a wide range of base-damage lesions (thymine glycols, UV-damaged lesions) as a base-damage-endonuclease.

Reason: AP-site endonuclease activity is a historically reported moonlighting activity. Its intrinsic catalytic relevance for human RPS3 in vivo is debated (PMID:18610840), so it is retained as a context-dependent non-core activity rather than a core function.

Summary: Mammalian RPS3 acts as a wide-range base-damage endonuclease, cleaving phosphodiester bonds in DNA containing various altered bases.

Reason: DNA endonuclease activity is a historically reported moonlighting activity whose physiological relevance in human cells is debated. Retained as a non-core, context-dependent activity.

Summary: Despite a sequence prediction of glycosylase activity, RPS3 does not have glycosylase activity; it acts as an endonuclease on damaged DNA.

Reason: The NOT annotation is well-supported and consistent with PMID:18610840: RPS3 lacks DNA glycosylase activity. Accept the negation.

Summary: RPS3 cleaves supercoiled UV-damaged DNA more efficiently than the relaxed counterpart, indicating a preference for/interaction with supercoiled DNA.

Reason: Supercoiled DNA binding is inferred from the preferential cleavage of supercoiled damaged DNA, part of RPS3's debated extra-ribosomal base-damage-endonuclease activity. Retained as non-core.

Summary: By surface plasmon resonance, human RPS3 binds 8-oxoG and AP sites with very high apparent affinity (orders of magnitude higher than OGG1).

Reason: Damaged DNA binding is among the best-supported extra-ribosomal activities of human RPS3, with quantitative binding data. It is secondary to the core ribosomal role; retained as non-core.

Summary: Human RPS3 binds 7,8-dihydro-8-oxoguanine (8-oxoG), an oxidized purine lesion, with high apparent affinity.

Reason: Oxidized purine (8-oxoG) DNA binding is directly and quantitatively supported; this term is more specific and accurate than the generic oxidized-pyrimidine term used elsewhere. It is an extra-ribosomal moonlighting activity, secondary to the core ribosomal function. Retained as non-core.

Summary: The earliest report implicating mammalian RPS3 in DNA damage processing identified an AP/UV endonuclease activity co-purifying with ribosomal protein S3.

Reason: This historical biochemical evidence connects RPS3 with AP/UV endonuclease activity, but the physiological relevance for human RPS3 is debated (PMID:18610840). Retained as a non-core, context-dependent activity.

Summary: RPS3 was detected in a high-throughput proteomic study of the membrane proteome of NK cells.

Reason: Detection of an abundant ribosomal protein in a membrane proteome most plausibly reflects co-isolation (e.g., membrane-associated ribosomes) or contamination rather than an RPS3-specific integral/peripheral membrane role. Treated as an over-annotation.

Summary: RPS3 directly associates with AUF1 and contributes to 3'UTR-dependent translation of Cry1 mRNA in the circadian clock context.

Reason: Generic protein binding term; the specific AUF1 association relates to translational regulation but is non-core relative to the structural ribosomal function and not a defining RPS3 molecular function. Retained as non-core.

Summary: Overexpression of GFP-RPS3 activates caspase-8/caspase-3 and sensitizes cells to cytokine-induced apoptosis, indicating a pro-apoptotic activity.

Reason: Pro-apoptotic activity is a context-dependent extra-ribosomal moonlighting function shown by overexpression/cytokine paradigms, secondary to the core ribosomal role. Retained as non-core.

Summary: RPS3 was identified as an mRNA-binding protein in a high-throughput interactome-capture atlas of mammalian mRNA-binding proteins.

Reason: RNA binding is consistent with RPS3's KH domain and its direct rRNA/mRNA contacts in the ribosome and in autoregulation (PMID:20217897). It is a real activity but, as captured by these broad mRNA-interactome screens, is secondary to the core structural ribosomal role; kept non-core for consistency with the other RNA binding annotations.

Summary: RPS3 was identified among the mRNA-bound proteome in a second high-throughput RNA-interactome study.

Reason: Independent HDA support for RPS3 RNA binding, consistent with its KH domain and rRNA/mRNA contacts. A real but broad MF, secondary to the structural ribosomal function; kept non-core for consistency with the other RNA binding annotations.

Summary: Human RPS3 has affinity for abasic sites and 8-oxoG residues and co-localizes with 8-oxoG damage foci after genotoxic stress.

Reason: Damaged DNA binding is a well-supported extra-ribosomal activity here complemented by in-cell co-localization with damage foci. Secondary to the core ribosomal role; retained as non-core.

Summary: RPS3 was observed in the nucleus as well as cytoplasm/cell periphery; in this study it colocalized with Nm23-H1 in the cell periphery and cytoplasm.

Reason: Nuclear localization is a regulated extra-ribosomal pool, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: Under basal conditions RPS3 is cytoplasmic/cytosolic, translocating to the nucleus only upon genotoxic stress.

Reason: Cytosol is the expected, core cellular location for RPS3's cytosolic ribosomal function, consistent with accepted cytosol annotations.

Summary: Human RPS3 physically interacts with the BER enzymes OGG1 and APE1/Ref-1 (co-immunoprecipitation and SPR).

Reason: Enzyme binding captures the directly-evidenced interactions with BER enzymes (OGG1, APE1), more informative than generic protein binding but part of RPS3's extra-ribosomal BER-cofactor role. Retained as non-core.

Summary: RPS3 was detected in a proteomic study of MHC class II-associated proteins in B-cell exosomes.

Reason: Detection of an abundant ribosomal protein in an exosome proteome is a common, non-specific finding and does not establish a discrete RPS3-specific exosomal function. Treated as an over-annotation.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a pre-40S/40S ribosome component) in the cytosol in the context of pre-rRNA processing during nucleus-to-cytosol translocation of pre-40S particles.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome, consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: Reactome places RPS3 (as a 40S/cytosolic ribosome component) in the cytosol within this translation/ribosome-associated pathway step.

Reason: Cytosol is the expected, core cellular location for RPS3 as part of the cytosolic ribosome participating in translation and ribosome-associated processes. Consistent with the accepted cytosol/cytosolic ribosome annotations.

Summary: RPS3 interacts with Nm23-H1 (a nucleoside diphosphate kinase) and modulates ERK signaling, reducing invasion of fibrosarcoma cells.

Reason: The specific kinase-related interaction documented in this reference is with Nm23-H1/ERK, not protein kinase A; the protein kinase A binding term is a questionable mapping. The genuine interaction (Nm23-H1) is an extra-ribosomal moonlighting context. Retained as non-core given the evidence supports a kinase-pathway interaction rather than this exact term.

Summary: H2S-mediated sulfhydration of the NF-kB p65 subunit at Cys38 promotes its binding to the coactivator RPS3, supporting an RPS3-p65 interaction in antiapoptotic NF-kB signaling.

Reason: Generic protein binding term; the specific RPS3-p65 interaction is part of RPS3's extra-ribosomal NF-kB coactivator role, captured more informatively by the NF-kB complex and transcription-regulation annotations. Retained as non-core.

Summary: RPS3 was identified as a component of IMP1 (IGF2BP1) mRNP granules, which contain ribosomal proteins and translation machinery.

Reason: RPS3 is a ribonucleoprotein-complex component (the ribosome itself is an RNP), so this broad term is correct; it is subsumed by the more specific cytosolic ribosome annotations. Consistent with the accepted IEA ribonucleoprotein complex annotation.

Summary: RPS3 was identified by protein sequencing and mass spectrometry as one of the proteins of the human 40S (small) ribosomal subunit.

Reason: This is the core cellular component for RPS3, directly evidenced by characterization of the human 40S ribosomal subunit proteins.

Summary: In eukaryotic initiation complexes, mRNA crosslinks to RPS3 (rpS3/S3p) at the mRNA entry channel of the 40S subunit, indicating direct mRNA contact.

Reason: RPS3 sits at the mRNA entry channel and directly contacts mRNA in the 40S subunit during initiation; mRNA binding is thus part of its core ribosomal structural/functional role at the decoding/entry site.

Summary: RPS3 was cloned and identified as the human S3 ribosomal protein, a structural component of the ribosome.

Reason: Structural constituent of ribosome is the core molecular function of RPS3, supported here by its identification as the human S3 ribosomal protein.

Summary: Endogenous RPS3 translocated into nuclei in cytokine-treated cells undergoing apoptosis.

Reason: Stimulus-dependent nuclear translocation in an apoptosis context is a regulated extra-ribosomal pool, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: RPS3 is present in the cytoplasm under basal conditions, with translocation to the nucleus during cytokine-induced apoptosis.

Reason: Cytoplasm is the expected, core cellular location for RPS3's cytosolic ribosomal function.

Summary: RPS3 localizes to the cytoplasm/cytosol and cell periphery, where it colocalizes with Nm23-H1.

Reason: Cytosol is the expected, core cellular location for RPS3's cytosolic ribosomal function.

Summary: RPS3 has an FXFP motif that serves as an ERK (MAP kinase) binding site, and ERK phosphorylates RPS3 at Thr42, as confirmed by co-immunoprecipitation.

Reason: Protein kinase binding captures the directly-evidenced ERK interaction that regulates RPS3 phosphorylation and its stress-induced nuclear translocation, an extra-ribosomal regulatory context. More informative than generic protein binding but non-core.

Summary: RPS3 was observed at the cell periphery in the context of its Nm23-H1 interaction and inhibition of invasion.

Reason: Ruffle membrane localization is a very specific term inferred from cell-periphery colocalization in an invasion assay; the evidence does not robustly establish stable ruffle-membrane residency of RPS3. Treated as an over-annotation.

Summary: An EPR study reported an apparent iron-sulfur-cluster signal in human RPS3, proposed in analogy to E. coli endonuclease III.

Reason: The iron-sulfur cluster claim is weakly supported and was not reproduced: refolding RPS3 with Fe2+/S2- did not increase activity and the protein's AP-lyase mechanism does not require a cluster (PMID:18610840). This is best treated as an over-annotation of a putative cofactor.

Summary: Human RPS3 binds 8-oxoG with high affinity; a single K132A change in its helix-hairpin-helix motif abolishes 8-oxoG binding while retaining AP-DNA-cleavage activity.

Reason: Damaged DNA binding is well-supported and mapped to a specific HhH DNA binding residue (K132). It is an extra-ribosomal moonlighting activity, secondary to the core ribosomal function. Retained as non-core.

Summary: Human RPS3 (and its K132A mutant) cleaves abasic DNA, an AP-lyase/AP-endonuclease-type activity; importantly, RPS3 binding to 8-oxoG can inhibit OGG1-mediated repair.

Reason: AP-site cleavage is supported, but the broader physiological significance of this activity is debated and context-dependent (RPS3 can inhibit rather than promote OGG1 repair). Retained as a non-core, context-dependent activity.

Summary: Lymphocyte-activating stimuli cause nuclear translocation of RPS3 (parallel to p65), where it forms part of NF-kB bound to specific chromatin regulatory sites.

Reason: Stimulus-dependent nuclear localization in the NF-kB context is a regulated extra-ribosomal pool, non-core relative to the cytosolic ribosomal location. Retained as non-core.

Summary: Genotoxic stress triggers ERK-dependent phosphorylation and nuclear translocation of RPS3 and its co-localization with 8-oxoG damage foci, placing it in a cellular DNA damage response pathway.

Reason: Participation in the DNA damage response is a regulated extra-ribosomal moonlighting role (damaged-DNA binding/relocalization), secondary to the core ribosomal function. Retained as non-core.

Summary: RPS3 knockdown increased survival of cells exposed to oxidative/alkylating genotoxic agents, and RPS3 inhibits OGG1 from liberating 8-oxoG, indicating RPS3 can negatively affect base-excision repair.

Reason: RPS3 can negatively regulate repair (by sequestering 8-oxoG lesions from OGG1), a context-dependent extra-ribosomal activity. Note this is opposite in sign to other reports where RPS3 stimulates repair (PMID:18973764), so the net effect is context-dependent. Retained as non-core.

Summary: RPS3 was identified by mass spectrometry as a protein of the human 40S ribosomal subunit in native and HCV IRES-bound complexes.

Reason: Structural constituent of ribosome is the core molecular function of RPS3, supported here by direct identification within the human 40S subunit.

Summary: RPS3 is a component of the human 40S (cytosolic small) ribosomal subunit, as identified by mass spectrometry of native and IRES-bound 40S complexes.

Reason: This is the core cellular component for RPS3, directly supported by compositional analysis of the human 40S subunit.