60S ribosomal export protein NMD3 is an essential protein required for cytoplasmic assembly and nuclear export of the 60S ribosomal subunit. Functions as a Crm1-dependent export adapter that binds nascent 60S particles and mediates their transport through nuclear pore complexes. Essential for ribosome biogenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Correctly identifies nuclear localization. IBA annotation is based on phylogenetic inference and is supported by experimental evidence showing NMD3 shuttles between nucleus and cytoplasm. Reason: NMD3 is explicitly documented in the literature as a shuttling protein that mediates nuclear export processes. The primary mapping places the functional nuclear localization signal (NLS) at aa 387-435 and the leucine-rich nuclear export signal (NES; INIDELLDEL) at aa 491-500. Supporting Evidence: PMID:11086007 We show here that Nmd3p shuttles PMID:11313466 Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nuclear export receptor Xpo1p |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: Correctly identifies cytoplasmic localization. NMD3 is present in both nucleus and cytoplasm, shuttling between compartments. Reason: NMD3 is a cytoplasmic protein that fractionates as a cytoplasmic factor and sediments in the position of free 60S subunits in sucrose gradients. Essential cytoplasmic role in stabilizing mature 60S subunits post-export. Supporting Evidence: PMID:10022925 Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients PMID:11086007 We show here that Nmd3p shuttles and that it is an essential adapter protein that provides the NES to direct nuclear export of nascent 60S subunits via the Crm1p pathway |
| GO:0000055 ribosomal large subunit export from nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Correct identification of core biological process. NMD3 is a key adapter protein for 60S subunit nuclear export, recruiting Crm1 export receptor. Reason: This is a central function of NMD3. Extensive experimental evidence demonstrates NMD3 is required for nuclear export of 60S subunits. Functions as Crm1-dependent adapter that directly binds to 60S subunits through rRNA contacts and provides nuclear export signal (NES) that is recognized by export receptor Crm1. Supporting Evidence: PMID:11086007 Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit PMID:11313466 Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p PMID:17347149 Nuclear export of the large (60S) ribosomal subunit depends on the adapter protein Nmd3 to provide a nuclear export signal (NES) file:yeast/NMD3/NMD3-deep-research-falcon.md Falcon synthesis supports Nmd3 as the conserved Crm1/Xpo1-dependent 60S ribosomal export adaptor. |
| GO:0043023 ribosomal large subunit binding | IBA GO_REF:0000033 | ACCEPT | Summary: Correct identification of protein-rRNA interaction. NMD3 directly binds the 60S subunit through multiple rRNA contact sites. Reason: NMD3 physically interacts with 60S subunits through direct binding to 25S rRNA helices. Nascent 60S subunits enter the free pool bound by Nmd3p. Coimmunoprecipitation experiments demonstrate specific interaction with 60S (not 40S) subunits. Supporting Evidence: PMID:11105761 The interaction was specific for 60S subunits; 40S subunits were not coimmunoprecipitated PMID:24240281 binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA |
| GO:0005654 nucleoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Correct identification of nucleoplasmic localization. NMD3 functions in nucleoplasm during pre-60S maturation and export preparation. Reason: UniProt-based IEA annotation is supported by functional studies showing NMD3 associates with nucleoplasmic pre-60S particles and is required for late nucleoplasmic maturation steps. CRAC analysis identified Nmd3 binding sites on nucleoplasmic pre-60S particles. Supporting Evidence: PMID:24240281 Nug2 binds the inter-subunit face of maturing, nucleoplasmic pre-60S particles, and the location clashes with the position of Nmd3 PMID:11086007 We show here that Nmd3p shuttles |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Duplicate IEA annotation for cytoplasm location. Acceptable as both annotations are correct. Reason: Redundant with IBA annotation to same term but both are correct. UniProt-based annotation confirms cytoplasmic localization. |
| GO:0015031 protein transport | IEA GO_REF:0000043 | MODIFY | Summary: Very broad annotation. NMD3 is specifically involved in ribosomal subunit transport, not general protein transport. Reason: While technically correct that NMD3 is involved in "protein transport" (as 60S is a protein complex), this term is too general and loses the critical specificity of the function. NMD3 is specifically involved in ribosomal subunit export, not general protein transport. Should be replaced with more specific term for 60S export. Proposed replacements: ribosomal large subunit export from nucleus |
| GO:0043023 ribosomal large subunit binding | IEA GO_REF:0000002 | ACCEPT | Summary: Correct but redundant with IDA annotations for same term. InterPro-based annotation is consistent with protein domain analysis. Reason: InterPro annotation IPR039768 correctly identifies NMD3 domain and its role in 60S binding. This is supported by experimental data showing direct rRNA binding. |
| GO:0005515 protein binding | IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... | MARK AS OVER ANNOTATED | Summary: Generic "protein binding" annotation derived from protein complex data. Annotation is too general; specific protein-interaction data should be used instead. Reason: While NMD3 does interact with ribosomal proteins (e.g., Rpl25p, Rpl10p), the generic "protein binding" term is uninformative and represents an over-annotation. The specific interactions are better captured by "ribosomal large subunit binding" (GO:0043023) which is already annotated. The PMID:16554755 reference is a global interactome study (yeast protein complexes) and does not provide mechanistic details about the binding function. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae |
| GO:0005515 protein binding | IPI PMID:21852791 The mRNA export factor Npl3 mediates the nuclear export of l... | MARK AS OVER ANNOTATED | Summary: Generic "protein binding" annotation. While NMD3 does interact with Npl3 and ribosomal proteins, the term is uninformative. Reason: NMD3 is reported to interact with Npl3 (mRNA export factor) in the context of 60S export, but this is a peripheral interaction to its core function. More specific molecular function terms exist (e.g., ribosomal large subunit binding, protein-macromolecule adaptor activity). Generic protein binding should be avoided when more specific terms are available and annotated. Supporting Evidence: PMID:21852791 The mRNA export factor Npl3 mediates the nuclear export of large ribosomal subunits |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MARK AS OVER ANNOTATED | Summary: Generic "protein binding" annotation from recent protein interactome study. Reason: PMID:37968396 provides global interactome structural information but does not specify functional protein-binding activity. Annotation of generic "protein binding" is not informative when more specific protein-interaction terms are already annotated (ribosomal large subunit binding, protein-macromolecule adaptor activity). Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome |
| GO:0030674 protein-macromolecule adaptor activity | IDA PMID:11086007 Nmd3p is a Crm1p-dependent adapter protein for nuclear expor... | ACCEPT | Summary: Excellent molecular function annotation. NMD3 directly functions as an adapter protein that bridges the 60S subunit to the Crm1 export receptor. Reason: NMD3 is functionally a protein-macromolecule adaptor that recruits the Crm1 export receptor to 60S subunits. The protein contains a functional nuclear export signal (NES) that directly recruits Crm1 while simultaneously bound to the 60S subunit. This is the defining characteristic of an adapter activity. Supporting Evidence: PMID:11086007 Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit PMID:17347149 the adapter protein Nmd3 to provide a nuclear export signal (NES). The leucine-rich NES is recognized by the export receptor Crm1 |
| GO:0030674 protein-macromolecule adaptor activity | IDA PMID:11313466 Nuclear export of 60s ribosomal subunits depends on Xpo1p an... | ACCEPT | Summary: Duplicate IDA annotation for adapter activity. Correctly identifies the molecular function. Reason: Second experimental source confirming adapter function. PMID:11313466 demonstrates NMD3 physically associates with ribosomal protein Rpl10p while functioning as an export adapter. Supporting Evidence: PMID:11313466 that associates with the large subunit protein Rpl10p...nuclear export sequence-containing factor |
| GO:0070180 large ribosomal subunit rRNA binding | IDA PMID:24240281 Coupled GTPase and remodelling ATPase activities form a chec... | ACCEPT | Summary: Excellent annotation specifying direct rRNA binding. CRAC and cross-linking data identify multiple specific binding sites. Reason: PMID:24240281 provides direct UV cross-linking (CRAC) evidence showing NMD3 contacts 25S rRNA at specific helix positions (H38, H69, H89). This is more specific and informative than generic protein binding and represents core structural contacts essential for function. Supporting Evidence: PMID:24240281 binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA |
| GO:0000055 ribosomal large subunit export from nucleus | IMP PMID:11086007 Nmd3p is a Crm1p-dependent adapter protein for nuclear expor... | ACCEPT | Summary: Correct experimental evidence for nuclear export function. IMP (Inferred from Mutant Phenotype) is appropriate evidence code. Reason: Temperature-sensitive nmd3 mutants are impaired in large subunit export, providing direct evidence for the functional requirement. This is a core biological process for NMD3. Supporting Evidence: PMID:11086007 We showed previously that a temperature sensitive nmd3 mutant failed to accumulate 60S subunits at nonpermissive temperature |
| GO:0000055 ribosomal large subunit export from nucleus | IGI PMID:23212245 Targeted proteomics reveals compositional dynamics of 60S pr... | ACCEPT | Summary: Duplicate annotation with IGI evidence from proteomics study of post-export particles. Appropriate evidence for genetic interaction data. Reason: PMID:23212245 provides genetic interaction evidence through targeted proteomics analysis of pre-60S particles after nuclear export, identifying factors required for coordinated export. IGI (Inferred from Genetic Interaction) appropriately codes genetic/proteomics interaction data. Supporting Evidence: PMID:23212245 Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export |
| GO:0005829 cytosol | IDA PMID:10022925 NMD3 encodes an essential cytoplasmic protein required for s... | ACCEPT | Summary: Correct identification of cytosolic localization. NMD3 fractionates with free 60S subunits in the cytosol. Reason: PMID:10022925 demonstrates by fractionation that Nmd3p sediments in sucrose gradients at the position of free 60S subunits in the cytosol, confirming cytosolic localization and association with mature subunits. Supporting Evidence: PMID:10022925 Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients |
| GO:0043023 ribosomal large subunit binding | IDA PMID:11105761 Nascent 60S ribosomal subunits enter the free pool bound by ... | ACCEPT | Summary: Correct identification of 60S binding. IDA evidence from coimmunoprecipitation experiments. Reason: PMID:11105761 demonstrates by coimmunoprecipitation that Nmd3p forms stable complex with free 60S subunits, with specific interaction for 60S (not 40S). Interaction occurs both with nascent and mature subunits. Supporting Evidence: PMID:11105761 Nmd3p forms a stable complex with free 60S subunits. Using an epitope-tagged Nmd3p, we show that free 60S subunits can be coimmunoprecipitated with Nmd3p |
| GO:0043023 ribosomal large subunit binding | IDA PMID:17347149 Novel interaction of the 60S ribosomal subunit export adapte... | ACCEPT | Summary: Duplicate IDA annotation for 60S binding from study of NPC interactions. Both confirm binding is core function. Reason: PMID:17347149 provides complementary evidence showing NMD3 binding to 60S subunit at nuclear pore complex, demonstrating binding occurs throughout the export process (nucleoplasm and at NPC). Supporting Evidence: PMID:17347149 Certain mutant Nmd3 proteins that are impaired for binding to the 60S subunit accumulate at the nuclear envelope |
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Experiment: Separate rRNA-binding from Crm1 recruitment by targeted Nmd3 NES and rRNA-contact mutants, then quantify effects on pre-60S export and cytosolic maturation.
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