NCU08990

UniProt ID: Q7S2X9
Organism: Neurospora crassa OR74A
Review Status: COMPLETE
📝 Provide Detailed Feedback

Gene Description

NCU08990 encodes Neurospora crassa eL39 (60S ribosomal protein L39), a 51-residue, highly basic structural protein of the cytosolic large ribosomal subunit. It is resolved as chain n1 in the cryo-EM structure of actively translating Neurospora 80S ribosomes (PDB 7R81). In the assembled large subunit eL39 lies in the polypeptide exit tunnel region; the orthologous budding-yeast protein is dispensable for viability but required for normal translational fidelity, resistance to paromomycin, normal subunit balance and growth in the cold. The protein therefore functions as a structural constituent of the cytoplasmic ribosome that contributes to the accuracy of cytoplasmic translation; like other ribosomal proteins it is assembled into the subunit while it is still a nuclear preribosome.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0002181 cytoplasmic translation
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT ancestral node PTN000463054 (PTHR19970) asserts cytoplasmic translation for eL39; NCU08990 is in the same PANTHER subfamily (SF0) as the human and yeast donors and is a resolved chain of the translating Neurospora 80S ribosome.
Reason: As a structural ribosomal protein eL39 does part of the work of translation (it is a component of the machine that performs it), so participation, not mere necessity, is established. Q7S2X9 carries the eL39 signatures (IPR000077, PF00832), is placed in PTHR19970:SF0 together with human RPL39 (P62891) and yeast RPL39 (P04650), and is mapped by UniProt to chain n1 of the Neurospora translating-ribosome cryo-EM structure 7R81. The yeast ortholog deletion shows a direct effect on translational accuracy. The PAINT spermatogenesis assertion on the eutherian RPL39L node (PTN004522638) was deliberately not placed at the root and is correctly not propagated to fungi.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
PMID:34815343
We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution.
PMID:10852723
Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type.
GO:0003735 structural constituent of ribosome
IBA
GO_REF:0000033 		ACCEPT
Summary: Core molecular function of eL39, inherited from the PTHR19970 root node and corroborated by the target's presence in the Neurospora 80S structure.
Reason: eL39 has no catalytic activity; its function is structural, as an integral protein of the large subunit. The PAINT node placement covers the whole eL39 clade (plant, mammalian and fungal seeds), Q7S2X9 is in SF0 with the characterized orthologs, and the protein is resolved in the Neurospora ribosome (7R81 chain n1).
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PANTHER; PTHR19970:SF0; LARGE RIBOSOMAL SUBUNIT PROTEIN EL39; 1.
PMID:10852723
Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy.
GO:0003735 structural constituent of ribosome
IEA
GO_REF:0000002 		ACCEPT
Summary: InterPro2GO mapping from the eL39 family signature IPR000077; agrees with the IBA row for the same term.
Reason: IPR000077 (Ribosomal_eL39) is specific to the eL39 family, all of whose characterized members are structural ribosomal proteins. Consistent with the IBA row and the 7R81 structure.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR InterPro; IPR000077; Ribosomal_eL39.
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
GO:0005840 ribosome
IEA
GO_REF:0000002 		MODIFY
Summary: Correct but general; eL39 is specifically a component of the cytosolic large ribosomal subunit, a term the gene already carries.
Reason: The InterPro2GO mapping gives only the generic ribosome. The eL39 family is a large-subunit family, and the Neurospora protein is resolved in the cytoplasmic 80S ribosome (7R81). The specific descendant GO:0022625 cytosolic large ribosomal subunit is already present on this gene (IBA, IEA) and is the appropriate refinement.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
PMID:10852723
Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy.
GO:0006412 translation
IEA
GO_REF:0000002 		MODIFY
Summary: Correct but general; the specific process is cytoplasmic translation, which the gene already carries by IBA.
Reason: eL39 is a component of the cytosolic (not mitochondrial) ribosome, so the general translation term should be refined to its descendant GO:0002181 cytoplasmic translation, already asserted on this gene by IBA.
Proposed replacements: cytoplasmic translation
Supporting Evidence:
PMID:34815343
We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution.
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
GO:0022625 cytosolic large ribosomal subunit
IBA
GO_REF:0000033 		ACCEPT
Summary: Root-node PAINT assertion seeded by both yeasts and mammals; NCU08990 sits in the same SF0 subfamily as the fungal seeds and is resolved in the Neurospora 60S subunit.
Reason: The node PTN000463054 includes fungal seeds (S. cerevisiae RPL39, S. pombe rpl39), both of which are in PTHR19970:SF0 like Q7S2X9. The target is chain n1 of the large subunit in the Neurospora 80S structure 7R81, which directly corroborates the inherited assertion.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
PMID:10852723
Protein L39 is the first protein of the 60S ribosomal subunit implicated in translational accuracy.
GO:0022625 cytosolic large ribosomal subunit
IEA
GO_REF:0000107 		ACCEPT
Summary: Ensembl Compara orthology transfer from S. cerevisiae RPL39 (P04650); consistent with the IBA row for the same term.
Reason: P04650 is a one-to-one fungal ortholog in the same PANTHER subfamily (PTHR19970:SF0), and the Neurospora protein is resolved in the large subunit of 7R81.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PDB; 7R81; EM; 2.70 A; n1=1-51.
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PANTHER; PTHR19970:SF0; LARGE RIBOSOMAL SUBUNIT PROTEIN EL39; 1.
GO:0030684 preribosome
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: Ensembl Compara transfer from S. pombe rpl39 (P05767, PTHR19970:SF0). Plausible, since ribosomal proteins are incorporated into nuclear pre-60S particles, but it describes a transient assembly state, not the site of the protein's function.
Reason: The orthology is sound (P05767 and Q7S2X9 are both in PTHR19970:SF0), and ribosomal proteins are incorporated during subunit assembly, so membership of a pre-60S particle is expected. No Neurospora preribosome experiment exists, and the donor annotation reflects assembly intermediates rather than eL39's function, which is exerted in the mature cytoplasmic ribosome. Kept as a non-core location.
Supporting Evidence:
file:NEUCR/NCU08990/NCU08990-uniprot.txt
DR PANTHER; PTHR19970:SF0; LARGE RIBOSOMAL SUBUNIT PROTEIN EL39; 1.

Core Functions

Structural constituent of the cytosolic 60S ribosomal subunit (eL39), resolved in the translating Neurospora 80S ribosome; contributes to the integrity and accuracy of cytoplasmic translation.

Molecular Function:
structural constituent of ribosome
Directly Involved In:
cytoplasmic translation
In Complex:
cytosolic large ribosomal subunit
Supporting Evidence:
  • file:NEUCR/NCU08990/NCU08990-uniprot.txt
    DR PDB; 7R81; EM; 2.70 A; n1=1-51.
  • PMID:34815343
    We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution.
  • PMID:10852723
    Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type.
  • file:NEUCR/NCU08990/NCU08990-uniprot.txt
    DR InterPro; IPR000077; Ribosomal_eL39.

References

Loading supporting content…

Download this section (compressed HTML)

Suggested Questions for Experts

Q: Does loss of NCU08990 in Neurospora (e.g. a knockout-collection strain, if viable) reproduce the increased misreading and paromomycin hypersensitivity seen for the yeast rpl39 deletion?

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML · NCU08990-protnlm-predictions-review.yaml · Review status: COMPLETE

NCU08990 encodes eL39, a small basic structural protein of the cytosolic large ribosomal subunit. It is present in the experimentally determined Neurospora 80S ribosome and participates in cytoplasmic protein synthesis. Characterized fungal eL39 contributes to ribosome integrity and translational accuracy.

Source documents: genes/NEUCR/NCU08990/NCU08990-protnlm-source.json · genes/NEUCR/NCU08990/NCU08990-uniprot.txt · genes/NEUCR/NCU08990/NCU08990-ai-review.yaml

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0005840 ribosome GO_CC
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-09 · file:NEUCR/NCU08990/NCU08990-protnlm-source.json
Review rationale: Neurospora cryo-EM structure 7R81 identifies this exact protein as eL39, entity 74/chain VB (author n1), in the translating large ribosomal subunit. The eL39-specific domain agrees with the direct structural assignment. GOA already provides cytosolic large ribosomal subunit (GO:0022625), a cellular-component descendant of ribosome. The emitted ribosome prediction is therefore correct but less precise than the established compartment and subunit assignment.
Supporting Evidence:
  • PMID:34815343: "We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution."
  • PMID:10852723: "Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type."
  • file:NEUCR/NCU08990/NCU08990-uniprot.txt: "DR InterPro; IPR000077; Ribosomal_eL39."
  • file:NEUCR/NCU08990/NCU08990-7R81-entity74.json: ""pdbx_strand_id": "n1" ... "pdbx_description": "60S ribosomal protein L39" ... "reference_database_accession": "Q7S2X9""
GO:1990904 ribonucleoprotein complex GO_CC
LSP — Less precise than existing annotation Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-09 · file:NEUCR/NCU08990/NCU08990-protnlm-source.json
Review rationale: Neurospora cryo-EM structure 7R81 identifies this exact protein as eL39, entity 74/chain VB (author n1), in the translating large ribosomal subunit. The eL39-specific domain agrees with the direct structural assignment. GOA already provides cytosolic large ribosomal subunit (GO:0022625), a cellular-component descendant of ribonucleoprotein complex. The emitted ribonucleoprotein complex prediction is therefore correct but less precise than the established compartment and subunit assignment.
Supporting Evidence:
  • PMID:34815343: "We elucidated CHX's mechanism of action based on the cryo-electron microscopy structure of actively translating Neurospora crassa ribosomes bound with CHX at 2.7-Å resolution."
  • PMID:10852723: "Each of the two L39 mutants displayed a 4-fold increase of their error frequencies over the wild type."
  • file:NEUCR/NCU08990/NCU08990-uniprot.txt: "DR InterPro; IPR000077; Ribosomal_eL39."
  • file:NEUCR/NCU08990/NCU08990-7R81-entity74.json: ""pdbx_strand_id": "n1" ... "pdbx_description": "60S ribosomal protein L39" ... "reference_database_accession": "Q7S2X9""

Deep Research

Falcon

(NCU08990-deep-research-falcon.md)

Loading supporting content…

Download this section (compressed HTML)

📚 Additional Documentation

Notes

(NCU08990-notes.md)

Loading supporting content…

Download this section (compressed HTML)

Protnlm Location Review

(NCU08990-protnlm-location-review.md)

Loading supporting content…

Download this section (compressed HTML)

📄 View Raw YAML

Loading supporting content…

Download this section (compressed HTML)