NMD3

UniProt ID: P38861
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
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Gene Description

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.

Existing Annotations Review

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.
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

Core Functions

NMD3 functions as a critical adapter protein that recruits the Crm1p export receptor to 60S ribosomal subunits, bridging the nascent 60S subunit to the nuclear export machinery via its leucine-rich NES motif

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.
  • file:yeast/NMD3/NMD3-deep-research-falcon.md
    Falcon literature synthesis supports Nmd3 as the conserved Crm1/Xpo1-dependent 60S ribosomal export adaptor.

NMD3 directly contacts 25S rRNA at multiple helix positions (H38, H69, H89) within the inter-subunit face of 60S particles, forming stable complexes with nascent and mature subunits

Supporting Evidence:
  • PMID:24240281
    binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA
  • PMID:11105761
    Nmd3p forms a stable complex with free 60S subunits.
  • file:interpro/panther/PTHR12746/PTHR12746-metadata.yaml
    PANTHER PTHR12746 is the conserved NMD3 family.

References

Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae.
Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit.
Nascent 60S ribosomal subunits enter the free pool bound by Nmd3p.
Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p, that associates with the large subunit protein Rpl10p.
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
Novel interaction of the 60S ribosomal subunit export adapter Nmd3 at the nuclear pore complex.
The mRNA export factor Npl3 mediates the nuclear export of large ribosomal subunits.
Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export.
Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export.
The social and structural architecture of the yeast protein interactome.
file:yeast/NMD3/NMD3-deep-research-falcon.md
Falcon deep research synthesis for NMD3
file:interpro/panther/PTHR12746/PTHR12746-metadata.yaml
PANTHER family PTHR12746 NMD3 metadata

Suggested Questions for Experts

Q: Should NMD3's rRNA-binding and adaptor activities both be retained as core molecular functions, or should the annotation emphasize adaptor activity as the primary function?

Suggested Experiments

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.

📚 Additional Documentation

Deep Research Falcon

(NMD3-deep-research-falcon.md)

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gene_id: NMD3
gene_symbol: NMD3
uniprot_accession: P38861
protein_description: 'RecName: Full=60S ribosomal export protein NMD3; AltName:
Full=Nonsense-mediated mRNA decay protein 3;'
gene_info: Name=NMD3; OrderedLocusNames=YHR170W;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Belongs to the NMD3 family. .
protein_domains: Nmd3. (IPR039768); Nmd3_N. (IPR007064); NMD3_OB. (IPR048898); NMD_SH3.
(IPR048899); NMD3 (PF04981)
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P38861
  • Protein Description: RecName: Full=60S ribosomal export protein NMD3; AltName: Full=Nonsense-mediated mRNA decay protein 3;
  • Gene Information: Name=NMD3; OrderedLocusNames=YHR170W;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the NMD3 family. .
  • Key Domains: Nmd3. (IPR039768); Nmd3_N. (IPR007064); NMD3_OB. (IPR048898); NMD_SH3. (IPR048899); NMD3 (PF04981)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "NMD3" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'NMD3' 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

Research Target:

Please provide a comprehensive research report on the gene NMD3 (gene ID: NMD3, UniProt: P38861) in yeast.

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.

Output

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.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

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.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P38861
  • Protein Description: RecName: Full=60S ribosomal export protein NMD3; AltName: Full=Nonsense-mediated mRNA decay protein 3;
  • Gene Information: Name=NMD3; OrderedLocusNames=YHR170W;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Belongs to the NMD3 family. .
  • Key Domains: Nmd3. (IPR039768); Nmd3_N. (IPR007064); NMD3_OB. (IPR048898); NMD_SH3. (IPR048899); NMD3 (PF04981)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "NMD3" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'NMD3' 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

Research Target:

Please provide a comprehensive research report on the gene NMD3 (gene ID: NMD3, UniProt: P38861) in yeast.

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.

Research report: NMD3 (YHR170W; UniProt P38861) in Saccharomyces cerevisiae

0. Target verification (gene/protein identity)

The literature summarized here refers to Saccharomyces cerevisiae Nmd3p (gene NMD3, ORF YHR170W), a conserved 60S ribosomal subunit export adaptor. This matches the UniProt description (P38861) of “60S ribosomal export protein NMD3” and the defining mechanistic features (Nmd3 family; nucleocytoplasmic shuttling; Crm1/Xpo1-dependent export; late pre-60S binding; release by Lsg1 and Rpl10/uL16) (gadal2001nuclearexportof pages 1-2, johnson2002nuclearexportof pages 2-3, malyutin2017nmd3isa pages 1-2).

1. Key concepts and definitions (current understanding)

1.1. What Nmd3 is (definition)

Nmd3p is an essential, conserved, shuttling adaptor protein required for nuclear export of nascent 60S ribosomal subunits. In yeast, it binds pre-60S particles and provides a leucine-rich nuclear export signal (NES) that recruits the export receptor Crm1/Xpo1 (gadal2001nuclearexportof pages 1-2, johnson2002nuclearexportof pages 2-3).

Although the gene symbol historically suggested a connection to nonsense-mediated decay, mechanistic work in yeast and reviews emphasize that its primary, essential function is ribosome large-subunit export and late maturation, not RNA decay catalysis (johnson2002nuclearexportof pages 2-3, gadal2001nuclearexportof pages 1-2).

1.2. Where Nmd3 acts in the 60S biogenesis pathway

Ribosome biogenesis in eukaryotes proceeds from nucleolus → nucleoplasm → cytoplasm; export of the large subunit through the nuclear pore complex (NPC) is a key transition. Nmd3 is best described as a late-acting “export competence” factor: it binds to large subunits and licenses Crm1-mediated export (johnson2002nuclearexportof pages 2-3, johnson2002nuclearexportof pages 1-2).

Reviews further frame Nmd3 as part of a quality control logic—binding preferentially to “mature/correctly folded” 60S particles and helping exclude immature ones from export (johnson2002nuclearexportof pages 1-2).

1.3. Export adaptor vs export receptor

  • Crm1/Xpo1 is the karyopherin-type export receptor that recognizes NES-bearing cargos in a RanGTP-dependent manner.
  • Nmd3 is a cargo-specific adaptor: it binds pre-60S and provides the NES in trans so Crm1 can engage the 60S particle (johnson2002nuclearexportof pages 2-3, gadal2001nuclearexportof pages 1-2).

2. Core functional annotation of yeast Nmd3p (mechanism and evidence)

2.1. Essentiality and role in 60S export

Genetic and cell biological evidence in yeast shows that impaired Nmd3 function causes nuclear accumulation of large-subunit reporters (export block). Gadal et al. used an in vivo export assay (Rpl25–GFP) and showed that thermosensitive nmd3 mutants impair 60S export, consistent with Nmd3 as an essential factor required for large-subunit export (gadal2001nuclearexportof pages 1-2).

2.2. Nmd3 binding site on the 60S subunit (structural/biochemical evidence)

A cryo-EM reconstruction of MBP-Nmd3 bound to the 60S subunit showed Nmd3 density on the intersubunit/joining face near 25S rRNA helices H38, H69, and H95, and Nmd3 binding is blocked when 60S is engaged in 80S ribosomes (consistent with a joining-face site) (sengupta2010characterizationofthe pages 1-2). The binding appears saturable at ~1:1 Nmd3:60S stoichiometry, even at 81-fold excess of Nmd3, and Nmd3 binds 60S but not 80S (sengupta2010characterizationofthe pages 1-2).

Visual evidence: A representative cryo-EM figure labeling helices H38/H69/H95 and showing the Nmd3 density on the 60S joining face is available from Sengupta et al. (sengupta2010characterizationofthe media 9c1f3f22).

2.3. Key interaction partners and their roles

Crm1/Xpo1 (export receptor)

Nmd3’s essential export function is mediated by Crm1/Xpo1, recruited through Nmd3’s C-terminal leucine-rich NES; the Crm1 dependence is a core feature of the pathway (gadal2001nuclearexportof pages 1-2, johnson2002nuclearexportof pages 2-3).

Rpl10/uL16 and Lsg1 (cytoplasmic recycling / maturation checkpoint)

After export to the cytoplasm, Nmd3 must be removed so the 60S can become translation competent. The release of Nmd3 from cytoplasmic 60S requires the ribosomal protein Rpl10/uL16 and the conserved cytoplasmic GTPase Lsg1 (hedges2005releaseofthe pages 1-2). Hedges et al. showed that defects in LSG1 or RPL10 impair Nmd3 recycling and 60S export, and that NMD3 overexpression or weakened Nmd3–60S binding alleles can suppress these defects—supporting a model where failure to recycle/release Nmd3 is a bottleneck (hedges2005releaseofthe pages 1-2).

High-resolution structures and biochemical reconstitution later clarified mechanistic details: Nmd3 occupies functional centers of the subunit (including E-site/P-site vicinity), and Nmd3–Lsg1 interactions remodel parts of the ribosome (including helix 69), consistent with a GTPase activation/coupling role for Lsg1 in Nmd3 eviction (malyutin2017nmd3isa pages 1-2).

Tif6/eIF6 (anti-association factor in late cytoplasmic maturation)

Cryo-EM of late cytoplasmic particles shows Nmd3 co-binding with Tif6/eIF6 and Lsg1; Nmd3 extends toward functionally important regions and contacts/relates to Tif6 positioning, consistent with coordinated late cytoplasmic maturation steps that must occur before subunit joining and translation (malyutin2017nmd3isa pages 1-2).

2.4. Domain architecture and shuttling signals (NLS/NES)

Reviews describe Nmd3 as having a conserved N-terminal domain (~40 kDa) and a eukaryote-specific C-terminal extension that contains both a basic NLS and leucine-rich NES required for nucleocytoplasmic shuttling (johnson2002nuclearexportof pages 2-3). The C-terminal NES is necessary for export: removal of the NES causes nuclear retention of the adaptor and 60S particles, while addition of a heterologous NES can restore export (johnson2002nuclearexportof pages 2-3).

A yeast-focused mechanistic synthesis (thesis excerpt) reports mapping of a C-terminal NLS (aa 399–419) and NES (aa 496–505); a canonical leucine-rich NES sequence is also described (LLDELDEMTL) (west2006nmd3pthenuclear pages 172-176).

2.5. Molecular mechanism from high-resolution cryo-EM (late cytoplasmic maturation)

Malyutin et al. reported that Nmd3 is a structural mimic of eIF5A and that its binding includes insertion into the ribosomal E site and stabilization/closure of the L1 stalk; other Nmd3 regions occupy/approach the P site and connect to Tif6-associated regions (malyutin2017nmd3isa pages 1-2). They reported cryo-EM structures of relevant complexes at 3.1 Å (60S–Nmd3) and 3.3 Å (60S–Nmd3–Lsg1–Tif6), helping explain how late cytoplasmic remodeling and factor release are coupled (malyutin2017nmd3isa pages 1-2).

3. Recent developments (prioritizing 2023–2024)

3.1. 2023: rRNA modification checkpoint upstream of Nmd3 export competence

Two 2023 studies provided strong evidence that a single rRNA 2′-O-methylation at Gm2922 gates late 60S biogenesis and nuclear export competence by controlling Nog2 behavior.

  • Yelland et al. (publication date: Dec 2023) showed that methylation of a single nucleotide in the large subunit catalytic center “gates ribosome assembly” and is needed for efficient nuclear export; they used massively parallel mutational scanning of Nog2 to identify bypass substitutions and used cryo-EM to visualize methylation-dependent structural engagement (yelland2023asingle2′omethylation pages 1-2). Because Nmd3 is loaded late in nuclear maturation, such checkpoints are directly relevant to the timing/availability of Nmd3 recruitment and subsequent export.
  • Sekulski et al. (publication date: May 2023) showed that loss of Spb1-dependent methylation leads to premature Nog2 activation and impaired recruitment/binding dynamics of Nog2 to nucleoplasmic intermediates, proposing a kinetic checkpoint near the nucleolar/nucleoplasmic boundary (sekulski2023rrnamethylationby pages 1-2).

These studies do not primarily re-characterize Nmd3 directly, but they reshape the current understanding of what makes a pre-60S particle “export-ready” for downstream export factors such as Nmd3.

3.2. 2023: quantitative live-cell export kinetics support cooperative CRM1 transport (conserved logic)

Junod et al. (publication date: Aug 2023) quantified pre-ribosome export dynamics by high-speed single-molecule microscopy in live mammalian cells. They report:
- ~two-thirds of NPC interactions lead to successful export.
- CRM1 inhibition reduces export efficiency 11–17-fold.
- CRM1 recognition of pre-60S is mediated by an NES on Nmd3, and they propose cooperative CRM1 usage to chaperone large cargo through the NPC (junod2023dynamicsofnuclear pages 1-3).

While this work is not in yeast, it provides an experimentally grounded quantitative framework for the conserved Nmd3–CRM1 axis.

3.3. 2024: conserved late-maturation factor biology around LSG1/NMD3

A 2024 study focused on human LSG1 reported that LSG1 is required for eviction/recycling of NMD3 in the cytoplasm, probing conserved biology of the LSG1–NMD3 stage of 60S maturation (junod2023dynamicsofnuclear pages 1-3). Although not yeast, it is relevant to interpreting yeast pathway conservation.

4. Current applications and real-world implementations

4.1. Experimental readouts for 60S export and export competence

Nmd3 is embedded in widely used experimental logic for ribosome export:
- Rpl25–GFP nuclear accumulation is used as a 60S export assay; nmd3 mutants cause nuclear retention of this reporter (gadal2001nuclearexportof pages 1-2).
- Structural studies use purified pre-60S/60S complexes containing Nmd3 to define late maturation states and factor occupancy, demonstrating that Nmd3 provides a tractable handle for isolating/export-competence states (sengupta2010characterizationofthe pages 1-2).

4.2. Generalizable nuclear export principles

Nmd3 is often cited as a canonical example of a cargo adaptor (providing an NES) enabling a general export receptor (Crm1) to transport a large RNP (60S) (johnson2002nuclearexportof pages 2-3). This makes Nmd3 a reference point in models of NPC transport specificity and large-cargo export.

5. Statistics and quantitative data points (from primary studies)

Key quantitative/structural datapoints available in the reviewed evidence include:
- Stoichiometry: Nmd3 binds 60S at a maximum ~1:1 stoichiometry, even at 81-fold excess Nmd3; binds 60S but not 80S (sengupta2010characterizationofthe pages 1-2).
- Cryo-EM resolution: 60S–Nmd3 at 3.1 Å and 60S–Nmd3–Lsg1–Tif6 at 3.3 Å (malyutin2017nmd3isa pages 1-2).
- Export efficiency (conserved, mammalian): ~two-thirds NPC interactions successful; CRM1 inhibition decreases efficiency 11–17-fold (junod2023dynamicsofnuclear pages 1-3).

6. Consolidated evidence table

Claim/finding Evidence type Key details/quantitative data System Primary citation with year URL
Nmd3 is the essential export adaptor for nascent 60S ribosomal subunits and functions with Xpo1/Crm1 Genetics, imaging Thermosensitive/dominant-negative nmd3 mutants caused nuclear accumulation of an Rpl25-GFP 60S reporter; Nmd3 associates with 60S and interacts with Rpl10/uL16 (gadal2001nuclearexportof pages 1-2) S. cerevisiae Gadal et al., 2001 (gadal2001nuclearexportof pages 1-2) https://doi.org/10.1128/mcb.21.10.3405-3415.2001
Nmd3 is a late-acting, conserved, CRM1-dependent shuttling factor with a eukaryote-specific C-terminal NLS/NES region Review Conserved N-terminal ~40-kDa domain; eukaryote-specific C-terminal extension contains a basic NLS and leucine-rich NES; NES deletion traps 60S in nucleus, while heterologous PKI NES rescues export (johnson2002nuclearexportof pages 2-3, johnson2002nuclearexportof pages 1-2) Yeast with conserved eukaryotic context Johnson et al., 2002 (johnson2002nuclearexportof pages 2-3, johnson2002nuclearexportof pages 1-2) https://doi.org/10.1016/S0968-0004(02)02208-9
Cytoplasmic release/recycling of Nmd3 from 60S requires Rpl10 and the cytoplasmic GTPase Lsg1 Genetics, cell biology, biochemistry In lsg1 or rpl10 mutants, Nmd3-GFP fails to recycle efficiently and 60S export is impaired; overexpression of NMD3 suppresses export defects; weaker 60S-binding Nmd3 mutants suppress lsg1/rpl10 defects (hedges2005releaseofthe pages 1-2) S. cerevisiae Hedges et al., 2005 (hedges2005releaseofthe pages 1-2) https://doi.org/10.1038/sj.emboj.7600547
Nmd3 binds the 60S subunit on the intersubunit/joining face near helices H38, H69, and H95 and binds at ~1:1 stoichiometry Cryo-EM, biochemistry Cryo-EM localized Nmd3 near 25S rRNA helices 38, 69, and 95; Nmd3 binds 60S but not 80S; maximum stoichiometry ~1:1 even at 81-fold excess Nmd3; N-terminal ~35 kDa contains two zinc-binding centers; NES mapped to aa 496–505 (sengupta2010characterizationofthe pages 1-2, sengupta2010characterizationofthe media 9c1f3f22) S. cerevisiae Sengupta et al., 2010 (sengupta2010characterizationofthe pages 1-2, sengupta2010characterizationofthe media 9c1f3f22) https://doi.org/10.1083/jcb.201001124
Nmd3 structurally mimics eIF5A and, together with Lsg1, remodels late cytoplasmic pre-60S particles Cryo-EM, in vitro biochemistry, genetics Cryo-EM structures of 60S–Nmd3 and 60S–Nmd3–Lsg1–Tif6 at 3.1 Å and 3.3 Å; Nmd3 inserts into the E site, contacts the P site and Tif6/eIF6, and helps activate Lsg1; free Lsg1 had no detectable GTP hydrolysis in vitro without the 60S/Nmd3 context (malyutin2017nmd3isa pages 1-2) S. cerevisiae Malyutin et al., 2017 (malyutin2017nmd3isa pages 1-2) https://doi.org/10.15252/embj.201696012
Nmd3 contains separable ribosome-binding and shuttling domains, including a canonical leucine-rich NES Mutational analysis, cell biology, biochemistry Thesis excerpt maps NLS to aa 399–419 and NES to aa 496–505; canonical NES sequence reported as LLDELDEMTL; NES deletion causes nuclear trapping of Nmd3 and 60S, whereas PKI NES fusion restores export; Kap123 implicated in import (west2006nmd3pthenuclear pages 38-43, west2006nmd3pthenuclear pages 172-176) S. cerevisiae West, 2006 thesis excerpt (west2006nmd3pthenuclear pages 38-43, west2006nmd3pthenuclear pages 172-176) N/A (thesis excerpt in current context)
A late nuclear checkpoint upstream of Nmd3 recruitment/export is set by Spb1-dependent methylation of G2922 controlling Nog2 behavior Cryo-EM, suppressor genetics, imaging Spb1-catalyzed methylation at G2922 prevents premature Nog2 GTPase activation; unmethylated G2922 in spb1D52A leads to impaired Nog2 binding to early nucleoplasmic pre-60S; proposed kinetic checkpoint before export-factor engagement (sekulski2023rrnamethylationby pages 1-2) S. cerevisiae Sekulski et al., 2023 (sekulski2023rrnamethylationby pages 1-2) https://doi.org/10.1038/s41467-023-36867-5
A single 2′-O-methylation at Gm2922 gates efficient 60S assembly and nuclear export, influencing the stage at which Nmd3 can load Mutational scanning, cryo-EM, genetics Loss of Gm2922 blocks pre-60S assembly and nuclear export; Nog2 bypass mutations were identified; cryo-EM visualized methylation-dependent insertion of Gm2922 into the Nog2 active-site channel; figures report ~3.1 Å structures (yelland2023asingle2′omethylation pages 1-2) S. cerevisiae Yelland et al., 2023 (yelland2023asingle2′omethylation pages 1-2) https://doi.org/10.1038/s41594-022-00891-8
Export of pre-60S particles is highly efficient and CRM1-dependent; Nmd3 provides the canonical CRM1-linked NES for pre-60S export Live-cell single-molecule imaging, smFRET In mammalian cells, about two-thirds of NPC interactions led to successful export; CRM1 inhibition reduced export efficiency by 11–17-fold; study explicitly cites Nmd3 NES as the CRM1-recognized signal on pre-60S (junod2023dynamicsofnuclear pages 1-3) Conserved eukaryote (mammalian cells; mechanism relevant to yeast Nmd3 pathway) Junod et al., 2023 (junod2023dynamicsofnuclear pages 1-3) https://doi.org/10.1016/j.isci.2023.107445

Table: This table compiles the main mechanistic and structural evidence supporting the role of yeast Nmd3/YHR170W as the essential 60S ribosomal export adaptor. It also highlights 2023 studies that refine the timing and checkpoints upstream or downstream of Nmd3-mediated export.

7. Limitations and scope notes

  • Many of the most quantitative export-dynamics measurements are currently available from mammalian imaging work (junod2023dynamicsofnuclear pages 1-3). Yeast-specific quantitative NPC transit statistics were not extracted from the available texts in this run.
  • A 2006 thesis excerpt is used for some NLS/NES mapping details (west2006nmd3pthenuclear pages 172-176); core pathway conclusions are corroborated by peer-reviewed primary and review literature (gadal2001nuclearexportof pages 1-2, johnson2002nuclearexportof pages 2-3, hedges2005releaseofthe pages 1-2, sengupta2010characterizationofthe pages 1-2, malyutin2017nmd3isa pages 1-2).

Key cited sources (with publication dates and URLs)

  • Gadal O. et al. 2001-05. Molecular and Cellular Biology. “Nuclear export of 60S ribosomal subunits depends on Xpo1p and requires… Nmd3p…” https://doi.org/10.1128/mcb.21.10.3405-3415.2001 (gadal2001nuclearexportof pages 1-2)
  • Johnson A.W. et al. 2002-11. Trends in Biochemical Sciences. “Nuclear export of ribosomal subunits.” https://doi.org/10.1016/S0968-0004(02)02208-9 (johnson2002nuclearexportof pages 2-3)
  • Hedges J. et al. 2005-02. The EMBO Journal. “Release of the export adapter, Nmd3p, from the 60S… requires Rpl10p and… Lsg1p.” https://doi.org/10.1038/sj.emboj.7600547 (hedges2005releaseofthe pages 1-2)
  • Sengupta J. et al. 2010-06. The Journal of Cell Biology. “Characterization of the nuclear export adaptor protein Nmd3…” https://doi.org/10.1083/jcb.201001124 (sengupta2010characterizationofthe pages 1-2)
  • Malyutin A.G. et al. 2017-02. The EMBO Journal. “Nmd3 is a structural mimic of eIF5A, and activates… Lsg1…” https://doi.org/10.15252/embj.201696012 (malyutin2017nmd3isa pages 1-2)
  • Sekulski K. et al. 2023-05. Nature Communications. “rRNA methylation by Spb1 regulates the GTPase activity of Nog2…” https://doi.org/10.1038/s41467-023-36867-5 (sekulski2023rrnamethylationby pages 1-2)
  • Yelland J.N. et al. 2023-12 (journal issue date shown; DOI indicates 2022 online publication). Nature Structural & Molecular Biology. “A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome.” https://doi.org/10.1038/s41594-022-00891-8 (yelland2023asingle2′omethylation pages 1-2)
  • Junod S.L. et al. 2023-08. iScience. “Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy…” https://doi.org/10.1016/j.isci.2023.107445 (junod2023dynamicsofnuclear pages 1-3)

References

  1. (gadal2001nuclearexportof pages 1-2): Olivier Gadal, Daniela Strauß, Jacques Kessl, Bernard Trumpower, David Tollervey, and Ed Hurt. Nuclear export of 60s ribosomal subunits depends on xpo1p and requires a nuclear export sequence-containing factor, nmd3p, that associates with the large subunit protein rpl10p. Molecular and Cellular Biology, 21:3405-3415, May 2001. URL: https://doi.org/10.1128/mcb.21.10.3405-3415.2001, doi:10.1128/mcb.21.10.3405-3415.2001. This article has 403 citations and is from a domain leading peer-reviewed journal.

  2. (johnson2002nuclearexportof pages 2-3): Arlen W Johnson, Elsebet Lund, and James Dahlberg. Nuclear export of ribosomal subunits. Trends in biochemical sciences, 27 11:580-5, Nov 2002. URL: https://doi.org/10.1016/s0968-0004(02)02208-9, doi:10.1016/s0968-0004(02)02208-9. This article has 211 citations and is from a domain leading peer-reviewed journal.

  3. (malyutin2017nmd3isa pages 1-2): Andrey G Malyutin, Sharmishtha Musalgaonkar, Stephanie Patchett, Joachim Frank, and Arlen W Johnson. Nmd3 is a structural mimic of eif5a, and activates the cpgtpase lsg1 during 60s ribosome biogenesis. The EMBO Journal, 36:854-868, Feb 2017. URL: https://doi.org/10.15252/embj.201696012, doi:10.15252/embj.201696012. This article has 89 citations.

  4. (johnson2002nuclearexportof pages 1-2): Arlen W Johnson, Elsebet Lund, and James Dahlberg. Nuclear export of ribosomal subunits. Trends in biochemical sciences, 27 11:580-5, Nov 2002. URL: https://doi.org/10.1016/s0968-0004(02)02208-9, doi:10.1016/s0968-0004(02)02208-9. This article has 211 citations and is from a domain leading peer-reviewed journal.

  5. (sengupta2010characterizationofthe pages 1-2): Jayati Sengupta, Cyril Bussiere, Jesper Pallesen, Matthew West, Arlen W. Johnson, and Joachim Frank. Characterization of the nuclear export adaptor protein nmd3 in association with the 60s ribosomal subunit. The Journal of Cell Biology, 189:1079-1086, Jun 2010. URL: https://doi.org/10.1083/jcb.201001124, doi:10.1083/jcb.201001124. This article has 92 citations.

  6. (sengupta2010characterizationofthe media 9c1f3f22): Jayati Sengupta, Cyril Bussiere, Jesper Pallesen, Matthew West, Arlen W. Johnson, and Joachim Frank. Characterization of the nuclear export adaptor protein nmd3 in association with the 60s ribosomal subunit. The Journal of Cell Biology, 189:1079-1086, Jun 2010. URL: https://doi.org/10.1083/jcb.201001124, doi:10.1083/jcb.201001124. This article has 92 citations.

  7. (hedges2005releaseofthe pages 1-2): John Hedges, Matthew West, and Arlen W Johnson. Release of the export adapter, nmd3p, from the 60s ribosomal subunit requires rpl10p and the cytoplasmic gtpase lsg1p. The EMBO Journal, 24:567-579, Feb 2005. URL: https://doi.org/10.1038/sj.emboj.7600547, doi:10.1038/sj.emboj.7600547. This article has 226 citations.

  8. (west2006nmd3pthenuclear pages 172-176): MB West. Nmd3p, the nuclear export adapter for the 60s ribosomal subunit: characterization of its recycling mechanism and novel interaction with the nuclear pore …. Unknown journal, 2006.

  9. (yelland2023asingle2′omethylation pages 1-2): James N. Yelland, Jack P. K. Bravo, Joshua J. Black, David W. Taylor, and Arlen W. Johnson. A single 2′-o-methylation of ribosomal rna gates assembly of a functional ribosome. Nature Structural & Molecular Biology, 30:91-98, Dec 2023. URL: https://doi.org/10.1038/s41594-022-00891-8, doi:10.1038/s41594-022-00891-8. This article has 42 citations and is from a highest quality peer-reviewed journal.

  10. (sekulski2023rrnamethylationby pages 1-2): Kamil Sekulski, Victor Emmanuel Cruz, Christine S. Weirich, and Jan P. Erzberger. Rrna methylation by spb1 regulates the gtpase activity of nog2 during 60s ribosomal subunit assembly. Nature Communications, May 2023. URL: https://doi.org/10.1038/s41467-023-36867-5, doi:10.1038/s41467-023-36867-5. This article has 15 citations and is from a highest quality peer-reviewed journal.

  11. (junod2023dynamicsofnuclear pages 1-3): Samuel L. Junod, Mark Tingey, Joseph M. Kelich, Alexander Goryaynov, Karl Herbine, and Weidong Yang. Dynamics of nuclear export of pre-ribosomal subunits revealed by high-speed single-molecule microscopy in live cells. iScience, 26:107445, Aug 2023. URL: https://doi.org/10.1016/j.isci.2023.107445, doi:10.1016/j.isci.2023.107445. This article has 9 citations and is from a peer-reviewed journal.

  12. (west2006nmd3pthenuclear pages 38-43): MB West. Nmd3p, the nuclear export adapter for the 60s ribosomal subunit: characterization of its recycling mechanism and novel interaction with the nuclear pore …. Unknown journal, 2006.

Citations

  1. johnson2002nuclearexportof pages 1-2
  2. gadal2001nuclearexportof pages 1-2
  3. sengupta2010characterizationofthe pages 1-2
  4. hedges2005releaseofthe pages 1-2
  5. johnson2002nuclearexportof pages 2-3
  6. sekulski2023rrnamethylationby pages 1-2
  7. junod2023dynamicsofnuclear pages 1-3
  8. https://doi.org/10.1128/mcb.21.10.3405-3415.2001
  9. https://doi.org/10.1016/S0968-0004(02
  10. https://doi.org/10.1038/sj.emboj.7600547
  11. https://doi.org/10.1083/jcb.201001124
  12. https://doi.org/10.15252/embj.201696012
  13. https://doi.org/10.1038/s41467-023-36867-5
  14. https://doi.org/10.1038/s41594-022-00891-8
  15. https://doi.org/10.1016/j.isci.2023.107445
  16. https://doi.org/10.1128/mcb.21.10.3405-3415.2001,
  17. https://doi.org/10.1016/s0968-0004(02
  18. https://doi.org/10.15252/embj.201696012,
  19. https://doi.org/10.1083/jcb.201001124,
  20. https://doi.org/10.1038/sj.emboj.7600547,
  21. https://doi.org/10.1038/s41594-022-00891-8,
  22. https://doi.org/10.1038/s41467-023-36867-5,
  23. https://doi.org/10.1016/j.isci.2023.107445,

📄 View Raw YAML

id: P38861
gene_symbol: NMD3
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: '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.'
core_functions:
  - molecular_function:
      id: GO:0030674
      label: protein-macromolecule adaptor activity
    description: NMD3 functions as a critical adapter protein that recruits the Crm1p export receptor to 60S ribosomal subunits, bridging the nascent 60S subunit to the nuclear export machinery via its leucine-rich NES motif
    directly_involved_in:
      - id: GO:0000055
        label: ribosomal large subunit export from nucleus
    locations:
      - id: GO:0005654
        label: nucleoplasm
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: PMID:11086007
        supporting_text: Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit.
      - reference_id: PMID:11313466
        supporting_text: Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p.
      - reference_id: file:yeast/NMD3/NMD3-deep-research-falcon.md
        supporting_text: Falcon literature synthesis supports Nmd3 as the conserved Crm1/Xpo1-dependent 60S ribosomal export adaptor.
  - molecular_function:
      id: GO:0070180
      label: large ribosomal subunit rRNA binding
    description: NMD3 directly contacts 25S rRNA at multiple helix positions (H38, H69, H89) within the inter-subunit face of 60S particles, forming stable complexes with nascent and mature subunits
    directly_involved_in:
      - id: GO:0000055
        label: ribosomal large subunit export from nucleus
    supported_by:
      - reference_id: PMID:24240281
        supporting_text: 'binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA'
      - reference_id: PMID:11105761
        supporting_text: Nmd3p forms a stable complex with free 60S subunits.
      - reference_id: file:interpro/panther/PTHR12746/PTHR12746-metadata.yaml
        supporting_text: PANTHER PTHR12746 is the conserved NMD3 family.
existing_annotations:
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11086007
        supporting_text: 'We show here that Nmd3p shuttles'
      - reference_id: PMID:11313466
        supporting_text: 'Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nuclear export receptor Xpo1p'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Correctly identifies cytoplasmic localization. NMD3 is present in both nucleus and cytoplasm, shuttling between compartments.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:10022925
        supporting_text: 'Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients'
      - reference_id: PMID:11086007
        supporting_text: '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'
- term:
    id: GO:0000055
    label: ribosomal large subunit export from nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Correct identification of core biological process. NMD3 is a key adapter protein for 60S subunit nuclear export, recruiting Crm1 export receptor.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11086007
        supporting_text: 'Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit'
      - reference_id: PMID:11313466
        supporting_text: 'Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p'
      - reference_id: PMID:17347149
        supporting_text: 'Nuclear export of the large (60S) ribosomal subunit depends on the adapter protein Nmd3 to provide a nuclear export signal (NES)'
      - reference_id: file:yeast/NMD3/NMD3-deep-research-falcon.md
        supporting_text: Falcon synthesis supports Nmd3 as the conserved Crm1/Xpo1-dependent 60S ribosomal export adaptor.
- term:
    id: GO:0043023
    label: ribosomal large subunit binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Correct identification of protein-rRNA interaction. NMD3 directly binds the 60S subunit through multiple rRNA contact sites.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11105761
        supporting_text: 'The interaction was specific for 60S subunits; 40S subunits were not coimmunoprecipitated'
      - reference_id: PMID:24240281
        supporting_text: 'binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA'
- term:
    id: GO:0005654
    label: nucleoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'Correct identification of nucleoplasmic localization. NMD3 functions in nucleoplasm during pre-60S maturation and export preparation.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:24240281
        supporting_text: 'Nug2 binds the inter-subunit face of maturing, nucleoplasmic pre-60S particles, and the location clashes with the position of Nmd3'
      - reference_id: PMID:11086007
        supporting_text: 'We show here that Nmd3p shuttles'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'Duplicate IEA annotation for cytoplasm location. Acceptable as both annotations are correct.'
    action: ACCEPT
    reason: 'Redundant with IBA annotation to same term but both are correct. UniProt-based annotation confirms cytoplasmic localization.'
- term:
    id: GO:0015031
    label: protein transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: 'Very broad annotation. NMD3 is specifically involved in ribosomal subunit transport, not general protein transport.'
    action: MODIFY
    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_replacement_terms:
      - id: GO:0000055
        label: ribosomal large subunit export from nucleus
    additional_reference_ids:
      - PMID:11086007
- term:
    id: GO:0043023
    label: ribosomal large subunit binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'Correct but redundant with IDA annotations for same term. InterPro-based annotation is consistent with protein domain analysis.'
    action: ACCEPT
    reason: 'InterPro annotation IPR039768 correctly identifies NMD3 domain and its role in 60S binding. This is supported by experimental data showing direct rRNA binding.'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: 'Generic "protein binding" annotation derived from protein complex data. Annotation is too general; specific protein-interaction data should be used instead.'
    action: MARK_AS_OVER_ANNOTATED
    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.'
    supported_by:
      - reference_id: PMID:16554755
        supporting_text: 'Global landscape of protein complexes in the yeast Saccharomyces cerevisiae'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21852791
  review:
    summary: 'Generic "protein binding" annotation. While NMD3 does interact with Npl3 and ribosomal proteins, the term is uninformative.'
    action: MARK_AS_OVER_ANNOTATED
    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.'
    supported_by:
      - reference_id: PMID:21852791
        supporting_text: 'The mRNA export factor Npl3 mediates the nuclear export of large ribosomal subunits'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: 'Generic "protein binding" annotation from recent protein interactome study.'
    action: MARK_AS_OVER_ANNOTATED
    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).'
    supported_by:
      - reference_id: PMID:37968396
        supporting_text: 'The social and structural architecture of the yeast protein interactome'
- term:
    id: GO:0030674
    label: protein-macromolecule adaptor activity
  evidence_type: IDA
  original_reference_id: PMID:11086007
  review:
    summary: 'Excellent molecular function annotation. NMD3 directly functions as an adapter protein that bridges the 60S subunit to the Crm1 export receptor.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11086007
        supporting_text: 'Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit'
      - reference_id: PMID:17347149
        supporting_text: 'the adapter protein Nmd3 to provide a nuclear export signal (NES). The leucine-rich NES is recognized by the export receptor Crm1'
- term:
    id: GO:0030674
    label: protein-macromolecule adaptor activity
  evidence_type: IDA
  original_reference_id: PMID:11313466
  review:
    summary: 'Duplicate IDA annotation for adapter activity. Correctly identifies the molecular function.'
    action: ACCEPT
    reason: 'Second experimental source confirming adapter function. PMID:11313466 demonstrates NMD3 physically associates with ribosomal protein Rpl10p while functioning as an export adapter.'
    supported_by:
      - reference_id: PMID:11313466
        supporting_text: 'that associates with the large subunit protein Rpl10p...nuclear export sequence-containing factor'
- term:
    id: GO:0070180
    label: large ribosomal subunit rRNA binding
  evidence_type: IDA
  original_reference_id: PMID:24240281
  review:
    summary: 'Excellent annotation specifying direct rRNA binding. CRAC and cross-linking data identify multiple specific binding sites.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:24240281
        supporting_text: 'binding sites, which were found to lie in H38, H69 and H89 of 25S rRNA'
- term:
    id: GO:0000055
    label: ribosomal large subunit export from nucleus
  evidence_type: IMP
  original_reference_id: PMID:11086007
  review:
    summary: 'Correct experimental evidence for nuclear export function. IMP (Inferred from Mutant Phenotype) is appropriate evidence code.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11086007
        supporting_text: 'We showed previously that a temperature sensitive nmd3 mutant failed to accumulate 60S subunits at nonpermissive temperature'
- term:
    id: GO:0000055
    label: ribosomal large subunit export from nucleus
  evidence_type: IGI
  original_reference_id: PMID:23212245
  review:
    summary: 'Duplicate annotation with IGI evidence from proteomics study of post-export particles. Appropriate evidence for genetic interaction data.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:23212245
        supporting_text: 'Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export'
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:10022925
  review:
    summary: 'Correct identification of cytosolic localization. NMD3 fractionates with free 60S subunits in the cytosol.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:10022925
        supporting_text: 'Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients'
- term:
    id: GO:0043023
    label: ribosomal large subunit binding
  evidence_type: IDA
  original_reference_id: PMID:11105761
  review:
    summary: 'Correct identification of 60S binding. IDA evidence from coimmunoprecipitation experiments.'
    action: ACCEPT
    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.'
    supported_by:
      - reference_id: PMID:11105761
        supporting_text: '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'
- term:
    id: GO:0043023
    label: ribosomal large subunit binding
  evidence_type: IDA
  original_reference_id: PMID:17347149
  review:
    summary: 'Duplicate IDA annotation for 60S binding from study of NPC interactions. Both confirm binding is core function.'
    action: ACCEPT
    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).'
    supported_by:
      - reference_id: PMID:17347149
        supporting_text: 'Certain mutant Nmd3 proteins that are impaired for binding to the 60S subunit accumulate at the nuclear envelope'
proposed_new_terms: []
suggested_questions:
- question: >-
    Should NMD3's rRNA-binding and adaptor activities both be retained as core
    molecular functions, or should the annotation emphasize adaptor activity as
    the primary function?
suggested_experiments:
- description: >-
    Separate rRNA-binding from Crm1 recruitment by targeted Nmd3 NES and
    rRNA-contact mutants, then quantify effects on pre-60S export and cytosolic
    maturation.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  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: PMID:10022925
  title: NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal
    subunits in Saccharomyces cerevisiae.
  findings: []
- id: PMID:11086007
  title: Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large
    ribosomal subunit.
  findings: []
- id: PMID:11105761
  title: Nascent 60S ribosomal subunits enter the free pool bound by Nmd3p.
  findings: []
- id: PMID:11313466
  title: Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a
    nuclear export sequence-containing factor, Nmd3p, that associates with the large
    subunit protein Rpl10p.
  findings: []
- id: PMID:16554755
  title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
  findings: []
- id: PMID:17347149
  title: Novel interaction of the 60S ribosomal subunit export adapter Nmd3 at the
    nuclear pore complex.
  findings: []
- id: PMID:21852791
  title: The mRNA export factor Npl3 mediates the nuclear export of large ribosomal
    subunits.
  findings: []
- id: PMID:23212245
  title: Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after
    nuclear export.
  findings: []
- id: PMID:24240281
  title: Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome
    export.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: file:yeast/NMD3/NMD3-deep-research-falcon.md
  title: Falcon deep research synthesis for NMD3
  findings: []
- id: file:interpro/panther/PTHR12746/PTHR12746-metadata.yaml
  title: PANTHER family PTHR12746 NMD3 metadata
  findings: []