NMD3 has four PAINT IBA rows and all are well placed.
PANTHER:PTN000297338 carries GO:0005634 nucleus and GO:0000055 ribosomal large subunit export from nucleus; the PAINT cache places these on a eukaryotic NMD3 ancestral node with Arabidopsis, yeast, and/or human descendant evidence. This matches the core shuttling-export role: PMID:11086007 and PMID:11313466.PANTHER:PTN000978434 carries GO:0005737 cytoplasm and GO:0043023 ribosomal large subunit binding across the NMD3 family. These are supported in yeast by fractionation and direct 60S binding evidence: PMID:10022925 and PMID:11105761.These are positive-control IBAs: the PAINT family is a dedicated NMD3 family, the yeast protein sits in the NMD3 subfamily, and there is no evidence of yeast-specific loss, paralog confusion, or compartment mismatch.
The IntAct-derived GO:0005515 protein binding rows from Krogan 2006, Hackmann 2011, and Michaelis 2023 were legacy MARK_AS_OVER_ANNOTATED calls. They should be REMOVE under the current project policy because GO:0005515 is uninformative, and the useful biology is already captured by NMD3's specific large-ribosomal-subunit-binding and protein-macromolecule-adaptor activities.
A search for 2024-2026 NMD3 yeast papers found recent 60S-biogenesis work upstream of Nmd3 loading and one direct 2025 preprint. Chitale et al. used an RPL10/uL16 loop mutation and found that simultaneous NMD3 and TIF6 mutations bypass a late cytoplasmic maturation arrest, allowing defective ribosomes into the translational pool PMID:41279726. This is consistent with the established Nmd3/Tif6 late-maturation checkpoint role, but it is a bioRxiv preprint and does not change any GO decisions here.
just fetch-gene yeast NMD3 --force refreshed NMD3 from 19 to 20 live GOA rows.
The four PTHR12746 IBA rows remain positive-control transfers on
PANTHER:PTN000297338 and PANTHER:PTN000978434; current PAINT drops the older
Arabidopsis donor from some WITH/FROM columns but leaves the target in the same
well-supported ancestral NMD3 clade.
Two exact historical source rows are no longer live in current GOA and were
kept with retired: true: the broad UniProt keyword GO:0015031 protein
transport row and the Krogan 2006 GO:0005515 protein binding row. Three
new IntAct GO:0005515 rows now assert Tif6 binding from PMID:18467557,
PMID:27251291, and PMID:37968396; all three were reviewed as REMOVE because
the interaction records are generic and Nmd3's informative molecular functions
are already captured by 60S-ribosomal-subunit binding and
protein-macromolecule adaptor activity.