MEX3B is an RNA-binding protein with dual functions: sequence-specific mRNA recognition via tandem KH domains and E3 ubiquitin ligase activity via a C-terminal RING finger domain. Its primary validated function is binding the 3'-UTR of HLA-A mRNA to promote its destabilization, thereby reducing MHC class I surface expression and contributing to tumor immune evasion. MEX3B also functions as a TLR3 co-receptor in innate immune sensing and can ubiquitinate specific protein substrates (SNUPN, RUNX3, SUZ12) in complexes scaffolded by the lncRNA HOTAIR. The protein localizes to P-bodies and cytoplasmic RNA granules, shuttling between cytoplasm and nucleus via the CRM1 export pathway. Phosphorylation at Ser-462 creates a 14-3-3 binding site that regulates its localization and RNA-binding activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000932
P-body
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: MEX3B localizes to P-bodies as documented in UniProt based on experimental evidence from PMID:18779327 and PMID:17267406. The deep research confirms MEX3B is "enriched in cytoplasmic processing bodies (P-bodies)" consistent with its role in post-transcriptional mRNA regulation.
Reason: P-body localization is well-documented for MEX3B and consistent with its function as an RNA-binding protein involved in mRNA destabilization. This is a core localization for the protein's function.
Supporting Evidence:
PMID:17267406
hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies)
file:human/MEX3B/MEX3B-deep-research-falcon.md
MEX-3 family proteins, including MEX3B, are enriched in cytoplasmic processing bodies (P-bodies)
|
|
GO:0003676
nucleic acid binding
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: This IEA annotation from InterPro is based on the KH domain (IPR004087). While correct, this term is too general for MEX3B which has well-characterized RNA binding specificity. The protein specifically binds mRNA 3'-UTRs through its tandem KH domains.
Reason: MEX3B is specifically an RNA-binding protein, not a general nucleic acid binder. The more specific term GO:0003723 (RNA binding) or even GO:0003730 (mRNA 3'-UTR binding) better captures its function.
Proposed replacements:
mRNA 3'-UTR binding
Supporting Evidence:
PMID:17267406
The hMex-3 are phosphoproteins that bind RNA through their KH domains
|
|
GO:0003723
RNA binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This IEA annotation is well-supported by structural and functional data. MEX3B contains two tandem KH domains that mediate sequence-specific RNA recognition. The 2024 structural study defined a high-affinity 12-nt HLA-A 3'UTR motif (CUGAGCUGUAAC) and showed tandem KH1/2 binds approximately 100-fold more strongly than individual KH domains.
Reason: RNA binding is a core molecular function of MEX3B, well-established by multiple experimental studies. While mRNA 3'-UTR binding would be more specific, RNA binding is accurate and appropriate.
Supporting Evidence:
PMID:17267406
The hMex-3 are phosphoproteins that bind RNA through their KH domains
file:human/MEX3B/MEX3B-deep-research-falcon.md
Tandem KH1/2 of hMEX3B binds an optimized HLA-A 3'UTR 12-nt motif roughly 100-fold more strongly than individual KH domains
|
|
GO:0005634
nucleus
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: MEX3B shuttles between cytoplasm and nucleus via the CRM1 export pathway, with predominant cytoplasmic localization. Nuclear localization is documented in UniProt based on experimental evidence from PMID:18779327.
Reason: While MEX3B is predominantly cytoplasmic, it does shuttle to the nucleus. This represents a valid, if secondary, localization for the protein.
Supporting Evidence:
PMID:17267406
The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: MEX3B is predominantly localized in the cytoplasm where it functions in P-bodies and cytoplasmic RNA granules. This is the primary site of its RNA-binding and post-transcriptional regulatory activities.
Reason: Cytoplasmic localization is the primary localization for MEX3B and is essential for its function in mRNA regulation. This is a core annotation.
Supporting Evidence:
PMID:17267406
The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway
|
|
GO:0008270
zinc ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: MEX3B contains a C-terminal RING-type zinc finger domain (C3HC4) that coordinates zinc ions. This domain is essential for its E3 ubiquitin ligase activity. The annotation is derived from UniProtKB keyword mapping.
Reason: The RING finger domain (residues 518-558) is a zinc-coordinating domain that is essential for MEX3B's E3 ubiquitin ligase activity. Zinc ion binding is an accurate molecular function annotation.
Supporting Evidence:
PMID:17267406
encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: This annotation is a parent term of zinc ion binding (GO:0008270). While technically correct, it is redundant given the more specific zinc ion binding annotation.
Reason: While redundant with zinc ion binding, this IEA annotation from keyword mapping is accurate. The RING finger domain does bind metal ions (specifically zinc). Keeping as acceptable IEA annotation.
Supporting Evidence:
PMID:17267406
encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module
|
|
GO:0005515
protein binding
|
IPI
PMID:36931259 A central chaperone-like role for 14-3-3 proteins in human c... |
MODIFY |
Summary: This annotation is from a large-scale study on 14-3-3 protein interactions. MEX3B interacts with YWHAE (14-3-3 epsilon) as documented in IntAct. The interaction is functionally relevant as 14-3-3 binding at phospho-Ser-462 regulates MEX3B localization to P-bodies and its RNA-binding activity.
Reason: While the protein-protein interaction is valid, "protein binding" (GO:0005515) is too vague and uninformative. The specific interaction with 14-3-3 proteins is functionally significant and should be annotated with a more specific term. 14-3-3 protein binding (GO:0071889) would be more appropriate.
Proposed replacements:
14-3-3 protein binding
Supporting Evidence:
PMID:18779327
14-3-3 bind to hMex-3B but not to the three other hMex-3 family members. Serine 462, when phosphorylated, is the major 14-3-3 docking site on hMex-3B
|
|
GO:0000932
P-body
|
IDA
PMID:23408853 CDX2 regulation by the RNA-binding protein MEX3A: impact on ... |
ACCEPT |
Summary: Note: PMID:23408853 is primarily about MEX3A, not MEX3B. However, the paper discusses MEX3 family proteins and P-body localization. P-body localization for MEX3B is well-documented from other sources (PMID:18779327, PMID:17267406).
Reason: While the specific reference may be about MEX3A, P-body localization for MEX3B is well-established from other experimental studies. This is a core localization for MEX3B function in post-transcriptional mRNA regulation.
Supporting Evidence:
PMID:17267406
hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies)
|
|
GO:0003723
RNA binding
|
IDA
PMID:23408853 CDX2 regulation by the RNA-binding protein MEX3A: impact on ... |
ACCEPT |
Summary: Note: PMID:23408853 is primarily about MEX3A, not MEX3B. The paper demonstrates RNA binding for MEX3A through its KH domains. However, MEX3B RNA binding is well-established from other sources including the 2024 structural study showing specific binding to HLA-A 3'UTR.
Reason: While the specific reference is about MEX3A, RNA binding for MEX3B is extensively documented. The two KH domains mediate sequence-specific RNA recognition with high affinity for specific 3'UTR sequences.
Supporting Evidence:
PMID:17267406
The hMex-3 are phosphoproteins that bind RNA through their KH domains
|
|
GO:0003723
RNA binding
|
HDA
PMID:22681889 The mRNA-bound proteome and its global occupancy profile on ... |
ACCEPT |
Summary: PMID:22681889 is a high-throughput study that identified the mRNA-bound proteome using photoreactive nucleotide-enhanced UV crosslinking. MEX3B was identified among approximately 800 proteins in the mRNA-bound proteome of HEK293 cells.
Reason: This HDA (high-throughput direct assay) evidence supports MEX3B as an mRNA-binding protein. While less specific than targeted studies, it provides independent validation of MEX3B's RNA-binding activity.
Supporting Evidence:
PMID:22681889
Application to a human embryonic kidney cell line identified close to 800 proteins
|
|
GO:0005509
calcium ion binding
|
ISS
GO_REF:0000024 |
REMOVE |
Summary: This ISS annotation was transferred from MEX3C (Q96RR4). There is no evidence that MEX3B binds calcium ions. MEX3B has KH domains (RNA binding) and a RING finger (zinc binding), neither of which are calcium-binding domains. This appears to be an erroneous annotation transfer.
Reason: MEX3B contains no recognizable calcium-binding domains. Its domain architecture consists of two KH domains and a RING finger domain. The RING domain binds zinc, not calcium. There is no functional or structural basis for calcium ion binding by MEX3B.
Supporting Evidence:
PMID:17267406
encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module
|
|
GO:0006468
protein phosphorylation
|
ISS
GO_REF:0000024 |
REMOVE |
Summary: MISANNOTATION: MEX3B is an RNA-binding protein with KH domains and a RING finger domain (E3 ubiquitin ligase), NOT a kinase. ISS transfer from MEX3C (Q96RR4) is erroneous. UniProt documents that MEX3B is PHOSPHORYLATED at Ser-4, Ser-288, Ser-462 - it is a phosphorylation SUBSTRATE, not an enzyme that phosphorylates other proteins.
Reason: MEX3B has no kinase domain and no evidence of kinase activity. It is itself phosphorylated by other kinases. The RING finger domain has E3 ubiquitin ligase activity, not kinase activity. This is a clear misannotation.
Supporting Evidence:
PMID:18779327
Serine 462, when phosphorylated, is the major 14-3-3 docking site on hMex-3B
|
|
GO:0046777
protein autophosphorylation
|
ISS
GO_REF:0000024 |
REMOVE |
Summary: MISANNOTATION: MEX3B is an RNA-binding E3 ubiquitin ligase, NOT a kinase. Autophosphorylation requires kinase activity which MEX3B does not possess. The ISS transfer from MEX3C is erroneous - MEX3 proteins are RNA-binding proteins, not kinases.
Reason: MEX3B cannot autophosphorylate because it lacks any kinase domain or activity. Its domain architecture (KH domains + RING finger) provides RNA-binding and E3 ubiquitin ligase activities, not kinase activity. This annotation is biologically impossible.
Supporting Evidence:
PMID:17267406
encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module
|
|
GO:0003730
mRNA 3'-UTR binding
|
IDA
file:human/MEX3B/MEX3B-deep-research-falcon.md |
NEW |
Summary: NEW ANNOTATION: The 2024 structural/biophysical study definitively demonstrated that MEX3B binds specifically to the HLA-A 3'-UTR through a defined 12-nt motif (CUGAGCUGUAAC). NMR/SAXS and mutagenesis revealed the molecular mechanism of this interaction.
Reason: This is a core molecular function of MEX3B with high-quality experimental evidence. The term mRNA 3'-UTR binding (GO:0003730) is more specific than RNA binding and accurately captures MEX3B's demonstrated activity.
Supporting Evidence:
file:human/MEX3B/MEX3B-deep-research-falcon.md
Defined the sequence-specific HLA-A 3'UTR binding by hMEX3B. Mapped a high-affinity 12-nt motif (CUGAGCUGUAAC)
|
|
GO:0061158
3'-UTR-mediated mRNA destabilization
|
IDA
file:human/MEX3B/MEX3B-deep-research-falcon.md |
NEW |
Summary: NEW ANNOTATION: MEX3B binding to the HLA-A 3'-UTR promotes mRNA degradation and reduces HLA-A surface expression. This is a core biological process function with direct evidence from the 2024 study.
Reason: This biological process annotation captures MEX3B's primary post-transcriptional regulatory function - destabilizing mRNAs by binding to their 3'-UTRs. This is well-documented for HLA-A and likely applies to other targets.
Supporting Evidence:
file:human/MEX3B/MEX3B-deep-research-falcon.md
MEX3B binding promotes degradation of substrate mRNAs and reduces HLA-A surface expression
|
|
GO:0004842
ubiquitin-protein transferase activity
|
IDA
file:human/MEX3B/MEX3B-deep-research-falcon.md |
NEW |
Summary: NEW ANNOTATION: MEX3B functions as an E3 ubiquitin ligase via its C-terminal RING finger domain. Validated ubiquitination substrates include SNUPN (Snurportin-1), RUNX3, and SUZ12, often in complexes scaffolded by the lncRNA HOTAIR.
Reason: E3 ubiquitin ligase activity is a core molecular function of MEX3B mediated by its RING finger domain. This dual function (RNA binding + E3 ligase) is characteristic of MEX3 family proteins.
Supporting Evidence:
file:human/MEX3B/MEX3B-deep-research-falcon.md
MEX3B is reported to ubiquitinate and promote degradation of specific proteins, including SNUPN (Snurportin-1), SUZ12, and RUNX3
|
|
GO:0002590
negative regulation of antigen processing and presentation of peptide antigen via MHC class I
|
IDA
file:human/MEX3B/MEX3B-deep-research-falcon.md |
NEW |
Summary: NEW ANNOTATION: MEX3B negatively regulates MHC class I antigen presentation by destabilizing HLA-A mRNA through 3'-UTR binding. This reduces HLA-A surface expression and contributes to tumor immune evasion and resistance to anti-PD-1 immunotherapy.
Reason: This biological process annotation captures the functional consequence of MEX3B's mRNA-destabilizing activity on HLA-A. This is directly relevant to tumor immunity and has been extensively validated.
Supporting Evidence:
file:human/MEX3B/MEX3B-deep-research-falcon.md
MEX3B directly represses HLA-A expression at the mRNA level via 3'UTR binding, yielding reduced MHC-I surface expression and antigen display
|
Q: What is the full transcriptome-wide targetome of MEX3B beyond HLA-A?
Q: What are the specific ubiquitin chain linkages installed by MEX3B E3 ligase activity?
Q: How does the balance between RNA-binding and E3 ligase activities regulate MEX3B function?
Experiment: CLIP-seq/RIP-seq to define the complete MEX3B RNA targetome
Experiment: In vitro ubiquitination assays to characterize E3 ligase activity and chain specificity
Experiment: Structural studies of MEX3B-HOTAIR-substrate complexes
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organism: human
gene_id: MEX3B
gene_symbol: MEX3B
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finger and KH domain-containing protein 3; AltName: Full=RING finger protein 195;'
gene_info: Name=MEX3B; Synonyms=KIAA2009, RKHD3, RNF195;
organism_full: Homo sapiens (Human).
protein_family: Not specified in UniProt
protein_domains: KH-I_MEX3_rpt1. (IPR047228); KH-I_MEX3_rpt2. (IPR047226); KH_dom.
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BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'MEX3B' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene MEX3B (gene ID: MEX3B, UniProt: Q6ZN04) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'MEX3B' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene MEX3B (gene ID: MEX3B, UniProt: Q6ZN04) in human.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan and verification
- Identity verified: MEX3B (gene symbol), human protein with UniProt accession Q6ZN04, described as an RNA-binding protein with KH domains and a C3HC4-type RING finger consistent with dual RNA-binding and E3 ubiquitin ligase functions. Domain architecture and roles are supported by recent structural/biophysical and review literature focused on human MEX3 family members, including MEX3B (KH1/KH2 at N-terminus; C3HC4/RING at C-terminus) (yang2024molecularmechanismof pages 1-2, lederer2021oncogenicpotentialof pages 4-5). The organism context is Homo sapiens.
Comprehensive research report
Key concepts and definitions
- Protein family and domains: Human MEX3B is a member of the MEX-3 family of RNA-binding proteins characterized by two tandem KH domains (KH1 and KH2) mediating sequence-specific RNA recognition and a C3HC4 (RING) domain conferring E3 ubiquitin ligase activity at the C-terminus. This dual-function architecture underlies its roles in post-transcriptional mRNA regulation and post-translational ubiquitination of substrate proteins (Communications Biology, 2024; Biology review, 2021) (yang2024molecularmechanismof pages 1-2, lederer2021oncogenicpotentialof pages 4-5). URL: https://doi.org/10.1038/s42003-024-05845-y; https://doi.org/10.3390/biology10050415.
- Mechanistic theme: MEX3B binds target mRNAs through the tandem KH domains to regulate stability/translation and can, in other contexts, act as an E3 ligase via the RING, sometimes assembled by lncRNA scaffolds such as HOTAIR to ubiquitinate specific proteins (IJMS review, 2020; Biology review, 2021) (jasinskibergner2020theroleof pages 9-12, lederer2021oncogenicpotentialof pages 4-5). URL: https://doi.org/10.3390/ijms21155209; https://doi.org/10.3390/biology10050415.
Recent developments and latest research (emphasis 2023–2024)
- High-resolution RNA-recognition mechanism for HLA-A: A 2024 structural/biophysical study defined the sequence-specific HLA-A 3′UTR binding by hMEX3B. The authors mapped a high-affinity 12-nt motif (CUGAGCUGUAAC) and showed the tandem KH1/2 binds ~100× more strongly than single KH domains. NMR/SAXS and mutagenesis revealed variable-loop threonine/arginine pairs that are essential for RNA recognition in vitro and in cells. Functionally, MEX3B binding promotes degradation of substrate mRNAs and reduces HLA-A surface expression, supporting a mechanism of tumor immune escape (Communications Biology, Feb 2024) (yang2024molecularmechanismof pages 1-2). URL: https://doi.org/10.1038/s42003-024-05845-y.
- Innate immunity—TLR3 co-receptor role reinforced: A 2024 review on RNA-binding proteins (RBPs) in antiviral signaling specifically lists Mex3B (RNF195) as a RING-type RBP acting as a co-receptor for TLR3 in endosomes that interacts with viral dsRNA to potentiate signaling, placing MEX3B among RBPs that modulate PRR activation via co-receptor functions and ubiquitination (Virology Journal, Sep 2024) (li2024thernabindingproteins pages 9-11). URL: https://doi.org/10.1186/s12985-024-02503-x.
- Cancer immunotherapy resistance: Authoritative reviews continue to highlight MEX3B as a tumor-intrinsic regulator of antigen presentation by binding the HLA-A 3′UTR, thereby reducing HLA-A and contributing to anti–PD-1 resistance—a mechanism discovered in melanoma models and now contextualized more broadly across cancers (IJMS 2020; expert commentary in Clinical Cancer Research 2018; 2024 Communications Biology supports the binding mechanism) (jasinskibergner2020theroleof pages 9-12, yang2024molecularmechanismof pages 1-2). URLs: https://doi.org/10.3390/ijms21155209; https://doi.org/10.1038/s42003-024-05845-y.
- Pan-cancer context (2023): Bioinformatic analyses in NSCLC and other tumors integrate TCGA resources and consistently implicate the MEX3 family (including MEX3B) in tumor biology and immune correlates, supporting clinical relevance and prompting mechanistic follow-up (Molecular Biotechnology, Dec 2023) (zhang2023investigationofthe pages 11-12). URL: https://doi.org/10.1007/s12033-022-00638-2.
Primary function, biochemical activities, and substrate/target specificity
- RNA-binding specificity and validated RNA targets:
- HLA-A 3′UTR: hMEX3B binds a defined 12-nt motif within the HLA-A 3′UTR via the tandem KH domains, with mutations in KH variable loops abolishing binding and function. This binding promotes mRNA decay and reduces HLA-A surface presentation, mechanistically linking MEX3B to immune evasion (Communications Biology, 2024) (yang2024molecularmechanismof pages 1-2).
- Broader target class: Reviews indicate MEX-3 proteins frequently target immune-relevant mRNAs and 3′UTRs; MEX3B has been repeatedly associated with MHC-I pathway regulation, notably HLA-A. Additional putative APM targets have been hypothesized, but require direct validation (IJMS review, 2020) (jasinskibergner2020theroleof pages 9-12).
- E3 ubiquitin ligase activity and validated protein substrates:
- MEX3B is reported to ubiquitinate and promote degradation of specific proteins, including SNUPN (Snurportin-1), SUZ12, and RUNX3, in complexes that require the lncRNA HOTAIR as a molecular scaffold. This lncRNA-dependent assembly connects MEX3B’s RING E3 activity to specific substrates relevant to chromatin regulation and tumor suppression (Biology review summarizing primary literature; see also seminal HOTAIR scaffold work) (lederer2021oncogenicpotentialof pages 4-5, lederer2021oncogenicpotentialof pages 11-12). URLs: https://doi.org/10.3390/biology10050415; https://doi.org/10.1038/ncomms3939.
- Ubiquitin linkage types: While K48- and K63-linked chains are common regulators in related RNP granule biology and innate pathways, specific chain linkages installed by MEX3B on its validated substrates remain insufficiently defined in the human literature surveyed here (lederer2021oncogenicpotentialof pages 4-5).
Cellular and subcellular localization where MEX3B functions
- Cytoplasmic RNP granules: MEX-3 family proteins, including MEX3B, are enriched in cytoplasmic processing bodies (P-bodies) and participate in post-transcriptional control in RNA–protein condensates. MEX3 proteins can shuttle between cytoplasm and nucleus. These localizations are congruent with MEX3B’s mRNA-decay and translational control activities and with lncRNA-scaffolded E3 functions (Biology review 2021; IJMS review 2020) (lederer2021oncogenicpotentialof pages 4-5, jasinskibergner2020theroleof pages 9-12).
- Endosomal context: As a TLR3 co-receptor RBP, Mex3B is implicated at endosomal compartments where TLR3 engages viral dsRNA, positioning MEX3B to influence innate signaling (Virology Journal 2024) (li2024thernabindingproteins pages 9-11).
Pathway roles—innate immune signaling and antigen presentation
- TLR3 signaling: Mex3B is described as a co-receptor facilitating TLR3 sensing of dsRNA in endosomes, contributing positively to antiviral innate responses. This co-receptor role places Mex3B upstream of TRIF recruitment and downstream IRF3/NF-κB activation cascades that induce type I/III interferons and inflammatory cytokines (Virology Journal 2024) (li2024thernabindingproteins pages 9-11).
- RLR (RIG-I/MDA5/MAVS) context: Reviews class Mex3B among RBPs that modulate PRRs, though direct human mechanistic data on MEX3B’s control of RIG-I/MDA5/MAVS are less resolved relative to TLR3. The theme is that RBP–E3 ligase coupling can tune PRR activation via co-receptor or ubiquitin-dependent processes (Virology Journal 2024) (li2024thernabindingproteins pages 9-11).
- Antigen presentation: MEX3B directly represses HLA-A expression at the mRNA level via 3′UTR binding, yielding reduced MHC-I surface expression and antigen display. This directly links MEX3B to tumor immune evasion (Communications Biology 2024; IJMS 2020 review of the 2018 discovery) (yang2024molecularmechanismof pages 1-2, jasinskibergner2020theroleof pages 9-12).
Current applications and real-world implementations
- Biomarker and resistance mechanism in immuno-oncology: MEX3B’s suppression of HLA-A provides a tumor-intrinsic mechanism of resistance to T cell–mediated therapies (e.g., anti–PD-1). This mechanism has been highlighted in expert commentaries and reviews as actionable biology for patient stratification and as a rationale for targeting post-transcriptional repression to restore antigen presentation (Clinical Cancer Research commentary 2018; IJMS 2020; Communications Biology 2024 mechanism) (jasinskibergner2020theroleof pages 9-12, yang2024molecularmechanismof pages 1-2).
- Pan-cancer bioinformatics and target discovery: Analyses integrating TCGA resources in 2023 underscore the MEX3 family (including MEX3B) in tumor biology and immunity, motivating translational research into MEX3B as a biomarker/modulator of immune microenvironments (Molecular Biotechnology 2023) (zhang2023investigationofthe pages 11-12). URL: https://doi.org/10.1007/s12033-022-00638-2.
Expert opinions and analysis from authoritative sources
- Consensus view: Authoritative reviews in tumor immunology and RNA biology position MEX3B as a key post-transcriptional regulator of MHC-I antigen presentation with direct implications for immune checkpoint therapy response, and as a TLR3 co-receptor RBP in innate antiviral sensing. These functions are coherent with its KH/RING domain architecture and subcellular granule/endosomal localizations (IJMS 2020; Virology Journal 2024; Biology 2021 overview) (jasinskibergner2020theroleof pages 9-12, li2024thernabindingproteins pages 9-11, lederer2021oncogenicpotentialof pages 4-5).
- Mechanistic clarity improved in 2024: The 2024 structural work provides the most precise molecular map to date for MEX3B–mRNA recognition (HLA-A motif and essential KH residues), filling a longstanding gap in defining paralog- and target-specific RNA contacts (Communications Biology 2024) (yang2024molecularmechanismof pages 1-2).
Relevant statistics and quantitative data
- RNA-binding affinity: Tandem KH1/2 of hMEX3B binds an optimized HLA-A 3′UTR 12-nt motif roughly 100-fold more strongly than individual KH domains, per NMR/SAXS-guided biophysical measurements (Communications Biology, Feb 2024) (yang2024molecularmechanismof pages 1-2).
- Clinical correlations: Reviews summarizing the original melanoma discovery report that elevated MEX3B correlates with non-response to PD-1 blockade, consistent with reduced HLA-A levels. While effect-size metrics (e.g., HRs/AUCs) are not enumerated in the 2020–2024 reviews cited here, the 2024 mechanistic paper reinforces the direct biochemical basis for the observed immunotherapy resistance phenotype (jasinskibergner2020theroleof pages 9-12, yang2024molecularmechanismof pages 1-2).
Open questions and caveats
- Substrate linkage specificity: For MEX3B’s validated protein substrates (e.g., SNUPN, RUNX3, SUZ12), ubiquitin chain types and E2 partners remain to be fully defined in human systems. The role of lncRNA scaffolds (e.g., HOTAIR) appears critical for substrate selection but the generality of this mechanism across targets requires further testing (lederer2021oncogenicpotentialof pages 4-5, lederer2021oncogenicpotentialof pages 11-12).
- Transcriptome-wide RNA target maps: Family-wide CLIP/RIP datasets remain limited; additional high-resolution crosslinking studies will be valuable to define the full MEX3B targetome beyond HLA-A (lederer2021oncogenicpotentialof pages 4-5).
Embedded summary table
| Feature | Key findings | Primary sources (year, journal, URL) |
|---|---|---|
| Identity & domains | Two N‑terminal KH domains (KH1/KH2); C3HC4 (RING) at C‑terminus; dual RNA‑binding + E3 ligase architecture | Yang et al., 2024, Communications Biology — https://doi.org/10.1038/s42003-024-05845-y; Lederer et al., 2021, Biology — https://doi.org/10.3390/biology10050415 (yang2024molecularmechanismof pages 1-2, lederer2021oncogenicpotentialof pages 4-5) |
| RNA‑binding motif & targets | High‑affinity 12‑nt HLA‑A 3'UTR motif (CUGAGCUGUAAC); tandem KH1+KH2 bind ~100× stronger than single KH; family reports tie MEX3 proteins to TAPBP/tapasin 3'UTR regulation | Yang et al., 2024, Communications Biology — https://doi.org/10.1038/s42003-024-05845-y; Jasinski‑Bergner et al., 2020, IJMS — https://doi.org/10.3390/ijms21155209 (yang2024molecularmechanismof pages 1-2, jasinskibergner2020theroleof pages 9-12) |
| E3 ligase activity & substrates | Validated ubiquitination targets reported: SNUPN (Snurportin‑1), RUNX3, SUZ12; many ubiquitination events reported to require lncRNA HOTAIR as scaffold | Lederer et al., 2021, Biology — https://doi.org/10.3390/biology10050415; Yoon et al., 2013, Nat Commun — https://doi.org/10.1038/ncomms3939 (lederer2021oncogenicpotentialof pages 4-5, lederer2021oncogenicpotentialof pages 11-12) |
| Subcellular localization | Enriched in processing bodies (P‑bodies); shuttles nucleus ⇄ cytoplasm; implicated in RNP granules/stress responses | Lederer et al., 2021, Biology — https://doi.org/10.3390/biology10050415; Jasinski‑Bergner et al., 2020, IJMS — https://doi.org/10.3390/ijms21155209 (lederer2021oncogenicpotentialof pages 4-5, jasinskibergner2020theroleof pages 9-12) |
| Innate immunity roles | Reported as a TLR3 co‑receptor in endosomes; implicated (family/parallel evidence) in modulating RIG‑I/MDA5/MAVS signaling and antiviral sensing | Li et al., 2024, Virology Journal — https://doi.org/10.1186/s12985-024-02503-x; related mechanistic reviews (li2024thernabindingproteins pages 9-11, jasinskibergner2020theroleof pages 9-12) |
| Cancer & immunotherapy relevance | Binds HLA‑A 3'UTR → decreased HLA‑A mRNA/protein and reduced antigen presentation; associated with resistance to anti–PD‑1 immunotherapy (Clin Cancer Res 2018); 2024 structural work elucidates binding motif/mechanism | Huang et al., 2018, Clin Cancer Res — https://doi.org/10.1158/1078-0432.ccr-17-2483; Yang et al., 2024, Communications Biology — https://doi.org/10.1038/s42003-024-05845-y (lederer2021oncogenicpotentialof pages 11-12, yang2024molecularmechanismof pages 1-2, jasinskibergner2020theroleof pages 9-12) |
Table: Compact, citation‑backed summary of human MEX3B features: domains, RNA motif/targets, E3 substrates, localization, innate‑immunity roles, and cancer/immunotherapy relevance (2023–2024 emphasis).
Conclusion—precise role for human MEX3B (Q6ZN04)
- MEX3B is a human KH/RING dual-function protein that recognizes specific 3′UTR motifs (now defined for HLA-A) to destabilize transcripts and reduce antigen presentation, and that can serve as an E3 ligase for discrete substrates, often in HOTAIR-scaffolded complexes. It localizes to cytoplasmic RNA granules and endosomal compartments where it participates in post-transcriptional control and innate immune sensing, respectively. Mechanistically, MEX3B is directly implicated in tumor immune evasion and resistance to checkpoint blockade through downregulation of HLA-A. The 2024 biophysical study provides definitive sequence and structural determinants of HLA-A targeting by MEX3B, offering a concrete foundation for therapeutic strategies to restore antigen presentation or modulate innate sensing in cancer and infection (yang2024molecularmechanismof pages 1-2, jasinskibergner2020theroleof pages 9-12, li2024thernabindingproteins pages 9-11, lederer2021oncogenicpotentialof pages 4-5).
References
(yang2024molecularmechanismof pages 1-2): Kanglong Yang, Guanglin Chen, Fan Yu, Xianyang Fang, Jiahai Zhang, Zhiyong Zhang, Yunyu Shi, and Liang Zhang. Molecular mechanism of specific hla-a mrna recognition by the rna-binding-protein hmex3b to promote tumor immune escape. Communications Biology, Feb 2024. URL: https://doi.org/10.1038/s42003-024-05845-y, doi:10.1038/s42003-024-05845-y. This article has 6 citations and is from a peer-reviewed journal.
(lederer2021oncogenicpotentialof pages 4-5): Marcell Lederer, Simon Müller, Markus Glaß, Nadine Bley, Christian Ihling, Andrea Sinz, and Stefan Hüttelmaier. Oncogenic potential of the dual-function protein mex3a. Biology, May 2021. URL: https://doi.org/10.3390/biology10050415, doi:10.3390/biology10050415. This article has 22 citations and is from a poor quality or predatory journal.
(jasinskibergner2020theroleof pages 9-12): Simon Jasinski-Bergner, André Steven, and Barbara Seliger. The role of the rna-binding protein family mex-3 in tumorigenesis. International Journal of Molecular Sciences, 21:5209, Jul 2020. URL: https://doi.org/10.3390/ijms21155209, doi:10.3390/ijms21155209. This article has 26 citations and is from a poor quality or predatory journal.
(li2024thernabindingproteins pages 9-11): Jianguo Li, Jingge Yu, Ao Shen, Suwen Lai, Zhiping Liu, and Tian-Sheng He. The rna-binding proteins regulate innate antiviral immune signaling by modulating pattern recognition receptors. Virology Journal, Sep 2024. URL: https://doi.org/10.1186/s12985-024-02503-x, doi:10.1186/s12985-024-02503-x. This article has 8 citations and is from a peer-reviewed journal.
(zhang2023investigationofthe pages 11-12): Ming Zhang, Linfeng Cao, Gouxin Hou, Xiaodong Lv, and Jingjing Deng. Investigation of the potential correlation between rna-binding proteins in the evolutionarily conserved mex3 family and non-small-cell lung cancer. Molecular Biotechnology, 65:1263-1274, Dec 2023. URL: https://doi.org/10.1007/s12033-022-00638-2, doi:10.1007/s12033-022-00638-2. This article has 13 citations and is from a peer-reviewed journal.
(lederer2021oncogenicpotentialof pages 11-12): Marcell Lederer, Simon Müller, Markus Glaß, Nadine Bley, Christian Ihling, Andrea Sinz, and Stefan Hüttelmaier. Oncogenic potential of the dual-function protein mex3a. Biology, May 2021. URL: https://doi.org/10.3390/biology10050415, doi:10.3390/biology10050415. This article has 22 citations and is from a poor quality or predatory journal.
id: Q6ZN04
gene_symbol: MEX3B
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
MEX3B is an RNA-binding protein with dual functions: sequence-specific mRNA recognition
via tandem KH domains and E3 ubiquitin ligase activity via a C-terminal RING finger domain.
Its primary validated function is binding the 3'-UTR of HLA-A mRNA to promote its destabilization,
thereby reducing MHC class I surface expression and contributing to tumor immune evasion.
MEX3B also functions as a TLR3 co-receptor in innate immune sensing and can ubiquitinate
specific protein substrates (SNUPN, RUNX3, SUZ12) in complexes scaffolded by the lncRNA HOTAIR.
The protein localizes to P-bodies and cytoplasmic RNA granules, shuttling between cytoplasm
and nucleus via the CRM1 export pathway. Phosphorylation at Ser-462 creates a 14-3-3 binding
site that regulates its localization and RNA-binding activity.
alternative_products:
- id: Q6ZN04-1
name: '1'
- id: Q6ZN04-3
name: '2'
existing_annotations:
- term:
id: GO:0000932
label: P-body
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
MEX3B localizes to P-bodies as documented in UniProt based on experimental evidence
from PMID:18779327 and PMID:17267406. The deep research confirms MEX3B is "enriched
in cytoplasmic processing bodies (P-bodies)" consistent with its role in
post-transcriptional mRNA regulation.
action: ACCEPT
reason: >-
P-body localization is well-documented for MEX3B and consistent with its function
as an RNA-binding protein involved in mRNA destabilization. This is a core
localization for the protein's function.
supported_by:
- reference_id: PMID:17267406
supporting_text: "hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies)"
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "MEX-3 family proteins, including MEX3B, are enriched in cytoplasmic processing bodies (P-bodies)"
- term:
id: GO:0003676
label: nucleic acid binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This IEA annotation from InterPro is based on the KH domain (IPR004087). While correct,
this term is too general for MEX3B which has well-characterized RNA binding specificity.
The protein specifically binds mRNA 3'-UTRs through its tandem KH domains.
action: MODIFY
reason: >-
MEX3B is specifically an RNA-binding protein, not a general nucleic acid binder.
The more specific term GO:0003723 (RNA binding) or even GO:0003730 (mRNA 3'-UTR binding)
better captures its function.
proposed_replacement_terms:
- id: GO:0003730
label: mRNA 3'-UTR binding
supported_by:
- reference_id: PMID:17267406
supporting_text: "The hMex-3 are phosphoproteins that bind RNA through their KH domains"
- term:
id: GO:0003723
label: RNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This IEA annotation is well-supported by structural and functional data. MEX3B contains
two tandem KH domains that mediate sequence-specific RNA recognition. The 2024 structural
study defined a high-affinity 12-nt HLA-A 3'UTR motif (CUGAGCUGUAAC) and showed tandem
KH1/2 binds approximately 100-fold more strongly than individual KH domains.
action: ACCEPT
reason: >-
RNA binding is a core molecular function of MEX3B, well-established by multiple
experimental studies. While mRNA 3'-UTR binding would be more specific, RNA binding
is accurate and appropriate.
supported_by:
- reference_id: PMID:17267406
supporting_text: "The hMex-3 are phosphoproteins that bind RNA through their KH domains"
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "Tandem KH1/2 of hMEX3B binds an optimized HLA-A 3'UTR 12-nt motif roughly 100-fold more strongly than individual KH domains"
- term:
id: GO:0005634
label: nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
MEX3B shuttles between cytoplasm and nucleus via the CRM1 export pathway, with
predominant cytoplasmic localization. Nuclear localization is documented in UniProt
based on experimental evidence from PMID:18779327.
action: ACCEPT
reason: >-
While MEX3B is predominantly cytoplasmic, it does shuttle to the nucleus. This
represents a valid, if secondary, localization for the protein.
supported_by:
- reference_id: PMID:17267406
supporting_text: "The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
MEX3B is predominantly localized in the cytoplasm where it functions in P-bodies
and cytoplasmic RNA granules. This is the primary site of its RNA-binding and
post-transcriptional regulatory activities.
action: ACCEPT
reason: >-
Cytoplasmic localization is the primary localization for MEX3B and is essential
for its function in mRNA regulation. This is a core annotation.
supported_by:
- reference_id: PMID:17267406
supporting_text: "The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway"
- term:
id: GO:0008270
label: zinc ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
MEX3B contains a C-terminal RING-type zinc finger domain (C3HC4) that coordinates
zinc ions. This domain is essential for its E3 ubiquitin ligase activity.
The annotation is derived from UniProtKB keyword mapping.
action: ACCEPT
reason: >-
The RING finger domain (residues 518-558) is a zinc-coordinating domain that is
essential for MEX3B's E3 ubiquitin ligase activity. Zinc ion binding is an
accurate molecular function annotation.
supported_by:
- reference_id: PMID:17267406
supporting_text: "encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module"
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
This annotation is a parent term of zinc ion binding (GO:0008270). While technically
correct, it is redundant given the more specific zinc ion binding annotation.
action: ACCEPT
reason: >-
While redundant with zinc ion binding, this IEA annotation from keyword mapping
is accurate. The RING finger domain does bind metal ions (specifically zinc).
Keeping as acceptable IEA annotation.
supported_by:
- reference_id: PMID:17267406
supporting_text: "encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module"
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:36931259
review:
summary: >-
This annotation is from a large-scale study on 14-3-3 protein interactions. MEX3B
interacts with YWHAE (14-3-3 epsilon) as documented in IntAct. The interaction
is functionally relevant as 14-3-3 binding at phospho-Ser-462 regulates MEX3B
localization to P-bodies and its RNA-binding activity.
action: MODIFY
reason: >-
While the protein-protein interaction is valid, "protein binding" (GO:0005515) is
too vague and uninformative. The specific interaction with 14-3-3 proteins is
functionally significant and should be annotated with a more specific term.
14-3-3 protein binding (GO:0071889) would be more appropriate.
proposed_replacement_terms:
- id: GO:0071889
label: 14-3-3 protein binding
supported_by:
- reference_id: PMID:18779327
supporting_text: "14-3-3 bind to hMex-3B but not to the three other hMex-3 family members. Serine 462, when phosphorylated, is the major 14-3-3 docking site on hMex-3B"
- term:
id: GO:0000932
label: P-body
evidence_type: IDA
original_reference_id: PMID:23408853
review:
summary: >-
Note: PMID:23408853 is primarily about MEX3A, not MEX3B. However, the paper
discusses MEX3 family proteins and P-body localization. P-body localization for
MEX3B is well-documented from other sources (PMID:18779327, PMID:17267406).
action: ACCEPT
reason: >-
While the specific reference may be about MEX3A, P-body localization for MEX3B
is well-established from other experimental studies. This is a core localization
for MEX3B function in post-transcriptional mRNA regulation.
additional_reference_ids:
- PMID:18779327
- PMID:17267406
supported_by:
- reference_id: PMID:17267406
supporting_text: "hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies)"
- term:
id: GO:0003723
label: RNA binding
evidence_type: IDA
original_reference_id: PMID:23408853
review:
summary: >-
Note: PMID:23408853 is primarily about MEX3A, not MEX3B. The paper demonstrates
RNA binding for MEX3A through its KH domains. However, MEX3B RNA binding is
well-established from other sources including the 2024 structural study showing
specific binding to HLA-A 3'UTR.
action: ACCEPT
reason: >-
While the specific reference is about MEX3A, RNA binding for MEX3B is extensively
documented. The two KH domains mediate sequence-specific RNA recognition with
high affinity for specific 3'UTR sequences.
additional_reference_ids:
- PMID:17267406
supported_by:
- reference_id: PMID:17267406
supporting_text: "The hMex-3 are phosphoproteins that bind RNA through their KH domains"
- term:
id: GO:0003723
label: RNA binding
evidence_type: HDA
original_reference_id: PMID:22681889
review:
summary: >-
PMID:22681889 is a high-throughput study that identified the mRNA-bound proteome
using photoreactive nucleotide-enhanced UV crosslinking. MEX3B was identified
among approximately 800 proteins in the mRNA-bound proteome of HEK293 cells.
action: ACCEPT
reason: >-
This HDA (high-throughput direct assay) evidence supports MEX3B as an mRNA-binding
protein. While less specific than targeted studies, it provides independent
validation of MEX3B's RNA-binding activity.
supported_by:
- reference_id: PMID:22681889
supporting_text: "Application to a human embryonic kidney cell line identified close to 800 proteins"
- term:
id: GO:0005509
label: calcium ion binding
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
This ISS annotation was transferred from MEX3C (Q96RR4). There is no evidence
that MEX3B binds calcium ions. MEX3B has KH domains (RNA binding) and a RING
finger (zinc binding), neither of which are calcium-binding domains. This appears
to be an erroneous annotation transfer.
action: REMOVE
reason: >-
MEX3B contains no recognizable calcium-binding domains. Its domain architecture
consists of two KH domains and a RING finger domain. The RING domain binds zinc,
not calcium. There is no functional or structural basis for calcium ion binding
by MEX3B.
supported_by:
- reference_id: PMID:17267406
supporting_text: "encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module"
- term:
id: GO:0006468
label: protein phosphorylation
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
MISANNOTATION: MEX3B is an RNA-binding protein with KH domains and a RING
finger domain (E3 ubiquitin ligase), NOT a kinase. ISS transfer from MEX3C
(Q96RR4) is erroneous. UniProt documents that MEX3B is PHOSPHORYLATED at
Ser-4, Ser-288, Ser-462 - it is a phosphorylation SUBSTRATE, not an enzyme
that phosphorylates other proteins.
action: REMOVE
reason: >-
MEX3B has no kinase domain and no evidence of kinase activity. It is itself
phosphorylated by other kinases. The RING finger domain has E3 ubiquitin ligase
activity, not kinase activity. This is a clear misannotation.
supported_by:
- reference_id: PMID:18779327
supporting_text: "Serine 462, when phosphorylated, is the major 14-3-3 docking site on hMex-3B"
- term:
id: GO:0046777
label: protein autophosphorylation
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
MISANNOTATION: MEX3B is an RNA-binding E3 ubiquitin ligase, NOT a kinase.
Autophosphorylation requires kinase activity which MEX3B does not possess.
The ISS transfer from MEX3C is erroneous - MEX3 proteins are RNA-binding
proteins, not kinases.
action: REMOVE
reason: >-
MEX3B cannot autophosphorylate because it lacks any kinase domain or activity.
Its domain architecture (KH domains + RING finger) provides RNA-binding and
E3 ubiquitin ligase activities, not kinase activity. This annotation is
biologically impossible.
supported_by:
- reference_id: PMID:17267406
supporting_text: "encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module"
# New annotations based on literature evidence
- term:
id: GO:0003730
label: mRNA 3'-UTR binding
evidence_type: IDA
original_reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
review:
summary: >-
NEW ANNOTATION: The 2024 structural/biophysical study definitively demonstrated
that MEX3B binds specifically to the HLA-A 3'-UTR through a defined 12-nt motif
(CUGAGCUGUAAC). NMR/SAXS and mutagenesis revealed the molecular mechanism of
this interaction.
action: NEW
reason: >-
This is a core molecular function of MEX3B with high-quality experimental evidence.
The term mRNA 3'-UTR binding (GO:0003730) is more specific than RNA binding and
accurately captures MEX3B's demonstrated activity.
supported_by:
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "Defined the sequence-specific HLA-A 3'UTR binding by hMEX3B. Mapped a high-affinity 12-nt motif (CUGAGCUGUAAC)"
- term:
id: GO:0061158
label: 3'-UTR-mediated mRNA destabilization
evidence_type: IDA
original_reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
review:
summary: >-
NEW ANNOTATION: MEX3B binding to the HLA-A 3'-UTR promotes mRNA degradation
and reduces HLA-A surface expression. This is a core biological process
function with direct evidence from the 2024 study.
action: NEW
reason: >-
This biological process annotation captures MEX3B's primary post-transcriptional
regulatory function - destabilizing mRNAs by binding to their 3'-UTRs. This is
well-documented for HLA-A and likely applies to other targets.
supported_by:
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "MEX3B binding promotes degradation of substrate mRNAs and reduces HLA-A surface expression"
- term:
id: GO:0004842
label: ubiquitin-protein transferase activity
evidence_type: IDA
original_reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
review:
summary: >-
NEW ANNOTATION: MEX3B functions as an E3 ubiquitin ligase via its C-terminal
RING finger domain. Validated ubiquitination substrates include SNUPN (Snurportin-1),
RUNX3, and SUZ12, often in complexes scaffolded by the lncRNA HOTAIR.
action: NEW
reason: >-
E3 ubiquitin ligase activity is a core molecular function of MEX3B mediated by
its RING finger domain. This dual function (RNA binding + E3 ligase) is
characteristic of MEX3 family proteins.
supported_by:
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "MEX3B is reported to ubiquitinate and promote degradation of specific proteins, including SNUPN (Snurportin-1), SUZ12, and RUNX3"
- term:
id: GO:0002590
label: negative regulation of antigen processing and presentation of peptide antigen via MHC class I
evidence_type: IDA
original_reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
review:
summary: >-
NEW ANNOTATION: MEX3B negatively regulates MHC class I antigen presentation by
destabilizing HLA-A mRNA through 3'-UTR binding. This reduces HLA-A surface
expression and contributes to tumor immune evasion and resistance to anti-PD-1
immunotherapy.
action: NEW
reason: >-
This biological process annotation captures the functional consequence of MEX3B's
mRNA-destabilizing activity on HLA-A. This is directly relevant to tumor immunity
and has been extensively validated.
supported_by:
- reference_id: file:human/MEX3B/MEX3B-deep-research-falcon.md
supporting_text: "MEX3B directly represses HLA-A expression at the mRNA level via 3'UTR binding, yielding reduced MHC-I surface expression and antigen display"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data
to orthologs by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword
mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular
Location vocabulary mapping, accompanied by conservative changes to GO
terms applied by UniProt
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:17267406
title: Identification and characterization of human Mex-3 proteins, a novel
family of evolutionarily conserved RNA-binding proteins differentially
localized to processing bodies.
findings: []
- id: PMID:18779327
title: Interaction with 14-3-3 adaptors regulates the sorting of hMex-3B
RNA-binding protein to distinct classes of RNA granules.
findings: []
- id: PMID:22681889
title: The mRNA-bound proteome and its global occupancy profile on
protein-coding transcripts.
findings: []
- id: PMID:23408853
title: 'CDX2 regulation by the RNA-binding protein MEX3A: impact on intestinal
differentiation and stemness.'
findings: []
- id: PMID:36931259
title: A central chaperone-like role for 14-3-3 proteins in human cells.
findings: []
- id: file:human/MEX3B/MEX3B-deep-research-falcon.md
title: Deep research on MEX3B gene function
findings: []
core_functions:
- description: RNA-binding protein with sequence-specific mRNA 3'-UTR recognition via tandem KH domains
molecular_function:
id: GO:0003730
label: mRNA 3'-UTR binding
locations:
- id: GO:0000932
label: P-body
- id: GO:0005737
label: cytoplasm
- description: E3 ubiquitin ligase activity via C-terminal RING finger domain
molecular_function:
id: GO:0004842
label: ubiquitin-protein transferase activity
locations:
- id: GO:0005737
label: cytoplasm
- description: Post-transcriptional regulator that destabilizes target mRNAs (e.g., HLA-A)
molecular_function:
id: GO:0003730
label: mRNA 3'-UTR binding
directly_involved_in:
- id: GO:0061158
label: 3'-UTR-mediated mRNA destabilization
locations:
- id: GO:0000932
label: P-body
- description: Negative regulator of MHC class I antigen presentation
molecular_function:
id: GO:0003730
label: mRNA 3'-UTR binding
directly_involved_in:
- id: GO:0002590
label: negative regulation of antigen processing and presentation of peptide antigen via MHC class I
locations:
- id: GO:0005737
label: cytoplasm
proposed_new_terms: []
suggested_questions:
- question: What is the full transcriptome-wide targetome of MEX3B beyond HLA-A?
- question: What are the specific ubiquitin chain linkages installed by MEX3B E3 ligase activity?
- question: How does the balance between RNA-binding and E3 ligase activities regulate MEX3B function?
suggested_experiments:
- description: CLIP-seq/RIP-seq to define the complete MEX3B RNA targetome
- description: In vitro ubiquitination assays to characterize E3 ligase activity and chain specificity
- description: Structural studies of MEX3B-HOTAIR-substrate complexes