NUP50 / Npap60 (Q9UKX7) - a MOBILE nuclear-basket nucleoporin in the pan-MLL-fusion core, and the evidence says basket, not nuclear envelope
also called NUP50 · Npap60 · NPAP60L · nucleoporin 50 · nuclear pore complex protein Nup50
NUP50 sits on the inside face of the nuclear pore but also moves off the pore into the nucleoplasm, and how much it moves depends on whether genes are being transcribed. It co-purifies with every MLL fusion tested - and the pattern of which OTHER pore proteins came along says this is not just membrane debris.
The same thing, for a scientist
NUP50 (Q9UKX7, 468 aa) is a mobile nucleoporin of the nucleoplasmic face, binds importin-alpha and Nup153, and shuttles between the NPC and the nucleoplasm in an RNA-polymerase-II-transcription-dependent way. In Skucha 2018 it co-purified with all seven MLL fusions, MLL-AF4 at p = 0.0121 (4|5), negative control 0|0. The dispatch question for this entry was whether the nucleoporin signal is a nuclear-envelope carry-over, and the complex-level answer - 5 of 27 nucleoporins, p = 0.0084, the weakest row in the table - was said to leave it open. Reading WHICH five settles it in the other direction: TPR (7 of 7 fusions), NUP50 (7) and NUP153 (4) are precisely the nuclear-basket and nucleoplasmic-face nucleoporins, all three with documented off-pore chromatin and gene-regulatory roles, while NUP160 and NUP43 appear at only 1 of 7. Zero FG central-channel nucleoporins (NUP62, NUP54, NUP58, NUP98, NUP214), zero transmembrane nucleoporins (POM121, NDC1) and no RANBP2 are present at any n. A bulk envelope carry-over would bring the abundant sticky central-channel FG nups first. It does not. The complex-wide p is weak because the complex is the wrong unit - the basket is the unit.
The Skucha row, stated in full
7 of 7 fusions. MLL-AF1p 0.0066 (6|5), MLL-AF4 0.0121 (4|5), MLL-AF9 0.0047 (11|9), MLL-CBP 0.0079 (5|8), MLL-EEN 0.0069 (12|12), MLL-ENL 0.0040 (10|11), MLL-GAS7 0.0302 (8|6); negative control 0|0 1. This is the most EVEN row in the tranche: every bait between 0.004 and 0.031, every bait between 9 and 24 total spectra. There is no bait-specific spike, which is what a shared, constitutive association looks like - and also what a shared contaminant looks like.
Basket, not envelope - and this is a measurement, not a preference
Counted by this beat from the 960-protein table on 2026-09-21. Of the 27 nucleoporins in the complex list, exactly five are in the network:
| nucleoporin | fusions | what it is |
|---|---|---|
| TPR | 7 | nuclear basket, the filament itself |
| NUP50 | 7 | nucleoplasmic face, mobile, importin-alpha binding |
| NUP153 | 4 | nuclear basket anchor, NUP50's own scaffold |
| NUP160 | 1 | Y-complex (Nup107-160) scaffold |
| NUP43 | 1 | Y-complex |
And the absences: no NUP62, NUP54, NUP58, NUP93, NUP205, NUP188, NUP155, NUP35, NUP85, NUP88, NUP107, NUP133, NUP214, NUP98, NUPL2, SEH1L, SEC13, AAAS, POM121, NDC1 or RANBP2 at any n. The three proteins recovered at 4-7 fusions are the three with the best-documented off-pore, intranuclear, gene-regulatory biology, and NUP153 is the specific scaffold that holds NUP50 3. The abundant FG central-channel nucleoporins that dominate any nuclear-envelope contamination are entirely missing.
So the dispatch premise - that a weak complex-wide signature leaves nuclear-envelope carry-over open - is not supported by the composition. The evidence falls against envelope carry-over. What it does not do is establish specific binding: the alternative that survives is that the fusion and these three nucleoporins share an intranuclear, transcription-associated pool, which is a substantive rival model and in several systems the more interesting one.
Why NUP50 is a plausible off-pore protein rather than a wall fragment
NUP50 has a pronounced presence both at the NPC and in the nucleoplasm and moves between them; its dynamic behaviour in both locations depends on active RNA polymerase II transcription and requires the N-terminal half of the protein, which contains the importin-alpha- and Nup153-binding domains - while being independent of importin-alpha, Nup153 and Nup98 themselves. Nup50 is also required for cell differentiation in C2C12 myoblasts without affecting proliferation 2. A separate study mapped the Nup153-Nup50 interface and showed a dual interaction: one site that targets Nup50 to the pore, and a second, importin-alpha-dependent site at the Nup153 distal tail, so Nup153 provides not only pore targeting but a local environment that brings Nup50 and importin-alpha together 3.
That second point connects two members of this tranche: KPNA2, importin-alpha-1, is also in the pan-fusion 42, and it is the only karyopherin of any kind in the whole 960-protein network.
The nucleoporin literature in this disease is all about NUP98, and that is a trap
(nucleoporin OR nucleoporins OR "nuclear pore")[tiab] against the KMT2A clause returns 18, and title-checking shows them to be overwhelmingly about NUP98 fusions, NUP98-KMT2A, NUP98-NSD1, and phase separation in NPM1-mutant AML. There is a real risk of reading 'nucleoporins matter in leukaemia' off that literature and attaching it to NUP50, which appears in none of it. The bare NUP50[tiab] OR NPAP60[tiab] query against the same clause returns 0.
| uniprot | Q9UKX7 |
|---|---|
| length AA | 468 |
| accession resolution | Resolved live 2026-09-21: gene_exact:NUP50 AND organism_id:9606 AND reviewed:true returns exactly ONE reviewed row, gene_primary NUP50, Q9UKX7, NUP50_HUMAN, 468 aa, synonym NPAP60L. Matches Skucha's table. Registry checked per rule 88: no row for NUP50 or NPAP60. Note that the yeast literature calls the ortholog Nup2, which is a different string and was searched separately. |
| localization | Nucleus, nuclear pore complex - UniProt Q9UKX7, ECO:0000269 PubMed 12802065; plus 'Nucleus membrane, peripheral membrane protein' by similarity (ECO:0000250). Fetched 2026-09-21. |
| subnuclear localization | NUCLEOPLASMIC FIBRILS OF THE NUCLEAR PORE COMPLEX - the basket side - by similarity in UniProt's note, with the experimental citation (PubMed 12802065) covering mitotic dissociation and telophase re-association rather than the resting address. A substantial mobile NUCLEOPLASMIC pool off the pore is established experimentally in the primary literature (PMID 24943837), and UniProt does not record it. That is a case of the standing rule that the database's annotation is a pointer, not the best available source. |
| localization shown for fusion | NO - nobody has imaged NUP50 in any KMT2A-rearranged cell. This graph carries localization-nuclear-envelope-proximity-kmt2a-amino-terminus and localization-nuclear-pore-nup98-fg-comparator; neither concerns NUP50. |
| shown for fusion | Co-purification with all seven MLL fusions including MLL-AF4 in Jurkat (p = 0.0121); shRNA-screened against MLL-AF9 in MOLM-13, score unpublished. NO independent experiment ties NUP50 to any KMT2A fusion. The nucleoporin literature in this disease is about NUP98 as a FUSION PARTNER, a different phenomenon. |
| selectivity | UNKNOWN - not named among the paper's controls and not known to be among the 40 re-screened. Must not reach a target list. |
| functional screen | FUNCTIONAL SCREEN. Supplementary Data 2 (file MOESM5) is the shRNA library for the negative-selection screen: 768 rows, 128 unique gene symbols, exactly six shRNAs per gene - counted by this beat on 2026-09-21. All 128 conserved interactors were screened in MLL-AF9-expressing MOLM-13 cells, and the paper says so in those words ('scoring of shRNA-induced effects upon knockdown of all 128 MLL-fusion interactors'). So this protein WAS functionally tested against an MLL fusion, which is more than a co-purification. But the per-gene result is published only as the heatmaps in Fig. 2c/2d, with no table of scores anywhere in the paper or its five supplementary files, so the outcome for this protein is not recoverable. Absence class for that number: measured-not-reported - an afternoon with the authors' source data would close it. |
| absence class | never-measured |
| absence class note | No instrument has been pointed at NUP50 in a KMT2A-rearranged cell outside the two screen hosts. The MOLM-13 shRNA score is separately measured-not-reported. PRIDE checked: PXD009338 is the only relevant deposition. |
| graph context | NUP50 appears in ZERO node files before this entry (id listing over 1,900 nodes, 2026-09-21). gene-tpr exists, written in cycle 47 from the same 42-protein set; NUP153 remains unwritten. |
skucha 2018
{
"bait": "MLL-AF4 (= KMT2A::AFF1)",
"p_value": 0.0121,
"spectral_counts": "4|5",
"n_fusions_of_seven": 7,
"negative_control_counts": "0|0",
"per_bait": {
"MLL-AF1p": "0.0066 (6|5)",
"MLL-AF4": "0.0121 (4|5)",
"MLL-AF9": "0.0047 (11|9)",
"MLL-CBP": "0.0079 (5|8)",
"MLL-EEN": "0.0069 (12|12)",
"MLL-ENL": "0.0040 (10|11)",
"MLL-GAS7": "0.0302 (8|6)"
},
"af4_spectral_rank_of_seven": 7,
"index_bait_note": "p = 0.0121. The most even row in this tranche: all seven baits within a factor of eight on p and within 9-24 total spectra.",
"source": "analyses/skucha-mll-fusion-interactome/results.json, re-derived from the cached MOESM4 xlsx 2026-09-21; run.py re-run, both controls PASS"
}nucleoporin composition
{
"question": "Is the nucleoporin signal a nuclear-envelope carry-over?",
"answer": "The composition says NO.",
"in_the_960": {
"TPR": 7,
"NUP50": 7,
"NUP153": 4,
"NUP160": 1,
"NUP43": 1
},
"absent_at_any_n": [
"NUP62",
"NUP54",
"NUP58",
"NUP93",
"NUP205",
"NUP188",
"NUP155",
"NUP35",
"NUP37",
"NUP85",
"NUP88",
"NUP107",
"NUP133",
"NUP214",
"NUP98",
"NUPL2",
"SEH1L",
"SEC13",
"AAAS",
"POM121",
"NDC1",
"RANBP2"
],
"reasoning": "The three nucleoporins recovered at 4-7 of 7 baits (TPR, NUP50, NUP153) are exactly the nuclear-basket and nucleoplasmic-face proteins with documented off-pore gene-regulatory function. Zero FG central-channel nucleoporins and zero transmembrane nucleoporins are present at any n, and those are the abundant, sticky species a bulk envelope carry-over would deliver first. The hypergeometric row (5 of 27, p = 0.0084) is weak because the 27-member nucleoporin list is the wrong unit; the basket is the unit.",
"what_this_does_not_establish": "It does not establish specific binding. The surviving alternative is a shared intranuclear transcription-associated pool, which is a substantive rival model rather than an artefact.",
"measured": "By this beat from the cached MOESM4 xlsx, 2026-09-21."
}cell types and states
[ "Jurkat (human T-ALL) - AP-MS host, nuclear lysate", "MOLM-13 (human MLL-AF9 AML) - shRNA screen host, six shRNAs, score unpublished", "C2C12 mouse myoblasts - differentiation requirement, transcription-dependent mobility", "cultured human cells - Nup153 interface mapping", "no leukaemia cell outside the two screen hosts, and no B-lineage KMT2A::AFF1 cell" ]
bounded literature
{
"query": "(NUP50[tiab] OR NPAP60[tiab]) AND (KMT2A[tiab] OR MLL[tiab] OR \"MLL-AF4\"[tiab] OR \"MLL-AF9\"[tiab] OR \"t(4;11)\"[tiab])",
"querytranslation": "(\"NUP50\"[Title/Abstract] OR \"NPAP60\"[Title/Abstract]) AND (\"KMT2A\"[Title/Abstract] OR \"MLL\"[Title/Abstract] OR \"MLL-AF4\"[Title/Abstract] OR \"MLL-AF9\"[Title/Abstract] OR \"t 4 11\"[Title/Abstract])",
"count": 0,
"date": "2026-09-21",
"tool": "NCBI esearch db=pubmed",
"names_tried": [
"NUP50",
"NPAP60",
"Nup2 (yeast ortholog, searched separately)"
],
"positive_control": "MEN1[tiab] AND the identical five-term clause returns 85.",
"complex_level_query": "Per the standing rule that a subunit absence must be checked at the complex level: (nucleoporin[tiab] OR nucleoporins[tiab] OR \"nuclear pore\"[tiab]) AND the same KMT2A clause returns 18 - NOT zero - and title-checking shows them to be about NUP98 fusions, NUP98-KMT2A, NUP98-NSD1, PRC1.1 antagonism and condensates in NPM1-mutant AML. None concerns NUP50. So the complex-level literature is real and is about a different protein, which is exactly the trap this rule exists to surface.",
"bound": "Titles and abstracts only; supporting figures not searched. Cytogenetic term quoted; querytranslation shows 't 4 11'[Title/Abstract] with no injected [UID] term."
}functionally screened in the source paper
{
"_added": "king, cycle 48, 2026-09-21, after Q86 flagged that cycle-47 entries understate the record. Verified by me directly from the supplementary file, not from the paper's prose.",
"screened": true,
"library_symbol": "NUP50",
"shrnas_for_this_gene": 6,
"design": "Supplementary Table 6 / MOESM5 is 768 data rows, 128 unique gene symbols, EXACTLY 6 shRNAs each -- counted with openpyxl on 2026-09-21. Negative-selection RNAi screen in MLL-AF9-expressing MOLM-13.",
"what_this_DOES_establish": "Every one of the 128 conserved MLL-fusion interactors, this protein included, was functionally tested against an MLL fusion. An entry saying 'nothing in the paper validates this prey' is true of BINDING and understates the record.",
"what_this_does_NOT_establish": "A per-gene result. Scores are presented as heatmaps (Fig. 2c/2d) and no per-gene depletion value is tabulated, so for any individual gene the outcome is measured-not-reported. It is also MLL-AF9 MOLM-13, a myeloid line, not the index fusion and not B-lineage.",
"absence_class_for_the_per_gene_score": "measured-not-reported"
}- Nucleoporins are structural and long-lived; there is no plausible acute pharmacology here, and an intervention would hit nucleocytoplasmic transport globally.
- Nup50 is required for differentiation in at least one lineage, so depleting it could deepen a differentiation block rather than relieve it - the opposite of what a menin inhibitor achieves.
- If the basket association is a shared intranuclear pool rather than a contact, an experiment designed to disrupt it would perturb transcription broadly and produce a phenotype that looks specific and is not.
- TPR and NUP50 are both pan-fusion and both nuclear-basket. Does the KMT2A::AFF1 fusion occupy basket-proximal chromatin? Nuclear-pore-associated gene positioning is measurable by DamID or by TPR ChIP in a t(4;11) line and has never been asked of this fusion.
- Is the NUP50-NUP153-KPNA2 trio one recovery of a pre-existing sub-assembly rather than three associations? Re-searching the PXD009338 spectra for the rest of the basket, below the top-300 cutoff, would show whether the basket is present as a graded signal or only as three proteins.
- NUP50 loss blocks differentiation in myoblasts without affecting proliferation. Differentiation block is the defining cell state of this disease - does NUP50 depletion affect differentiation in a KMT2A-rearranged blast?
- Why is there no FG central-channel nucleoporin in this network at all, when NUP98's FG domain is the transforming element of the NUP98 fusions? A negative that a comparison across the two fusion families could make informative.
- E1moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paper
NUP50 co-purified with all seven Strep-HA-tagged MLL fusions expressed as single-copy transgenes in isogenic human Jurkat T-ALL cells; for MLL-AF4 (= KMT2A::AFF1) the combined p-value is 0.0121 with spectral counts 4|5 and a negative control of 0|0.
MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. · Skucha A, Ebner J, Schmoellerl J, Roth M, Eder T, Cesar-Razquin A, Stukalov A, Vittori S, Muhar M, Lu B, Aichinger M, Jude J, Mueller AC, Gyorffy B, Vakoc CR, Valent P, Bennett KL, Zuber J, Superti-Furga G, Grebien F · Nature Communications 2018What this evidence cannot show
SYSTEM: the AP-MS host is JURKAT, a human T-ALL line, while KMT2A::AFF1 disease is B-lineage infant leukaemia; a partner requiring a B-cell or infant proteome cannot appear here and a T-lineage partner can appear spuriously. The bait is a Strep-HA-tagged, SINGLE-COPY, doxycycline-induced transgene at an FRT/Flp cassette, not the endogenous fusion. Prey came from bulk nuclear lysate (buffer C420, 420 mM NaCl) after a single STREP-Tactin step, so co-purification is NOT evidence of a direct contact. INCLUSION RULE: the paper kept the top 300 interactions per bait by combined p-value rather than applying a p threshold (Methods, verbatim: "All the identified bait-prey pairs were ranked by the combined p-value. The 300 most significant interactions per bait were retained."). Measured by this beat from the cached MOESM4 xlsx on 2026-09-21: 545 of the 2,049 per-bait p-values in the table (26.6%) exceed 0.05; within the MLL-AF4 column alone it is 186 of 291 (63.9%), and that column's maximum p is 0.175. MEASURED BY THIS BEAT, 2026-09-21, from the cached MOESM4 xlsx: across all 42 pan-fusion proteins the MLL-AF4 column carries the LOWEST total spectral counts of the seven baits for 34 of 42, and is sixth or seventh for 40 of 42. That is a bait-level property (transgene expression, purification depth or the DDX5/DDX17 GLM normalisation), not a statement about any one prey, so a low MLL-AF4 count must not be read as a weaker association than the same protein's count under another bait. For NUP50 the MLL-AF4 total (9 spectra over two replicates) is rank 7 of the seven baits, against a maximum of 24 under another bait. All seven per-bait values, p (replicate spectral counts): MLL-AF1p 0.0066 (6|5); MLL-AF4 0.0121 (4|5); MLL-AF9 0.0047 (11|9); MLL-CBP 0.0079 (5|8); MLL-EEN 0.0069 (12|12); MLL-ENL 0.0040 (10|11); MLL-GAS7 0.0302 (8|6). SPECIFIC TO THIS PROTEIN: this is the most uniform row in the tranche - all seven baits between p = 0.004 and 0.031 and between 9 and 24 total spectra, with no bait-specific spike. Uniformity across seven structurally unrelated baits is what a constitutive association looks like and is equally what a shared background protein looks like; the negative control is 0|0, which argues against the latter but does not settle it. SELECTIVITY: the paper's named non-selectivity controls are RFC1, SF3A3 and CCT3 - knockdown inhibited MLL-wild-type K562 and HL-60 as much as MOLM-13 - against MEN1 as the selective positive. Only 40 of the 128 ('the 40 candidate genes with the highest confidence') entered that MLL-r versus MLL-wild-type re-screen, and the paper does not list which 40. This protein is not named among the controls, but that is NOT evidence of selectivity: it is equally consistent with the protein never having reached the second screen. Recorded as unknown, and this entry must not be read as nominating a target. Values re-read from the cached xlsx on 2026-09-21 and cross-checked against analyses/skucha-mll-fusion-interactome/results.json, whose two controls (128 proteins shared by >=5 baits and 42 by all seven, both matching the paper; MEN1 present with all seven) both PASS on today's re-run.
Evidence that argues against this (2)
- IntAct has never curated this dataset, so no independent curator has re-examined these calls and no interactome-coverage metric built on IntAct can see them; the raw spectra at ProteomeXchange PXD009338 have not been reanalysed here. The authors themselves removed seven proteins from the shared set by hand as 'either frequently observed contaminants or ... not detected in human hematopoietic cell lines', which concedes that the rank cutoff lets contaminants through - and ACTB survived that filter, sitting in the pan-fusion 42 with a NON-ZERO negative control (3|3). Ten of the 42 carry a non-zero negative control: PSIP1 0|5, MCM2 0|2, ACTB 3|3, CSNK2A1 2|0, RUNX1 0|2, SF3A3 0|3, TCEB3 0|1, CHD4 2|2, SMARCC1 1|0, ZNF512 0|2 - counted by this beat from the xlsx neg_ctrl column, 2026-09-21. ProteomeXchange/PRIDE 2018
- The paper states that 'more than one third of proteins in the network of conserved MLL-fusion protein interaction partners were identified as essential in recent genome-wide screens'. Abundance and essentiality both raise the odds of recovery in an AP-MS experiment, so membership in the conserved core is partly a statement about how much of a protein is present in a nucleus, not only about what it binds. Skucha A et al. 2018
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Nup50 is a mobile nucleoporin present both at the nuclear pore complex and in the nucleoplasm and moving between them; its dynamic behaviour in both locations depends on active RNA polymerase II transcription and requires its N-terminal half, while being independent of importin-alpha, Nup153 and Nup98; Nup50 depletion in C2C12 myoblasts blocks differentiation without affecting proliferation.
Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. · Buchwalter AL, Liang Y, Hetzer MW · Mol Biol Cell 2014What this evidence cannot show
Mouse C2C12 myoblasts and cultured cells, 2014; photobleaching-based dynamics, which measure mobility rather than occupancy, and a differentiation assay in a muscle lineage. Not haematopoietic, not a fusion system. Cited here for one thing: that NUP50 has a substantial off-pore nucleoplasmic pool whose behaviour is coupled to transcription, which is what makes a nucleoporin in a chromatin-protein purification something other than membrane debris. Read from the abstract.
Evidence that argues against this (1)
- Transcription-dependent mobility is also shown for Nup153 and Nup98 in the same study, so it is a property of a class of mobile nucleoporins rather than something that singles out NUP50 - and NUP98's own leukaemogenic biology is entirely as a fusion partner, which is a different phenomenon from what is claimed here. Makise M et al. 2012
- E3strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
Nup153 provides the scaffold for Nup50 through a dual interface: a site in Nup153's unique N-terminal region that is critical for Nup50's pore localisation, and a second site at Nup153's distal tail that is importin-alpha-dependent, so that the partnership both targets Nup50 to the pore and creates a local environment bringing Nup50 and importin-alpha together.
The Nup153-Nup50 protein interface and its role in nuclear import. · Makise M, Mackay DR, Elgort S, Shankaran SS, Adam SA, Ullman KS · J Biol Chem 2012What this evidence cannot show
Cultured human cells with domain-mapping and import assays, 2012; an in vitro and cell-biological mapping, not a structure. Not haematopoietic, not a fusion system. Read from the abstract. Cited here because NUP153 is in the Skucha network at 4 of 7 fusions and KPNA2 (importin-alpha-1) at 7 of 7, so the paper describes a documented three-way relationship among proteins that all appear in the same purification - which is a reason to treat them as one observation rather than three.
Evidence that argues against this (1)
- Three proteins that bind each other will co-purify with anything that pulls down one of them, so the joint presence of NUP50, NUP153 and KPNA2 is at least as easily read as one recovery of a pre-existing sub-assembly as three independent associations with the fusion. That reading weakens rather than strengthens the case that the fusion contacts any of them. Skucha A et al. 2018
co-purified, all 7 MLL fusions, Jurkat AP-MS, MLL-AF4 p=0.0121 (4|5)
- co-occurs with →TPR / Megator (P12270) - the nuclear-basket nucleoporin that builds heterochromatin exclusion zones, in the pan-MLL-fusion core
the two pan-fusion nuclear-basket nucleoporins; no FG central-channel nup is in the network at any n
a nucleoporin in the interactome that is NOT an FG nup and is not a fusion partner
composition of the recovered nucleoporins argues against envelope carry-over and for the basket
importin-alpha binds NUP50 and the NUP153 distal tail; all three are in this network