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NUBP1

gene
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Also known as NBP35CIAO5

Summary

NUBP1 (NUBP iron-sulfur cluster assembly factor 1, cytosolic, HGNC:8041) is a protein-coding gene on chromosome 16p13.13, encoding Cytosolic Fe-S cluster assembly factor NUBP1 (P53384). Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. It is a common-essential gene (DepMap: required in 96.5% of cancer cell lines).

NUBP1 is a member of the NUBP/MRP subfamily of ATP-binding proteins (Nakashima et al., 1999 [PubMed 10486206]).

Source: NCBI Gene 4682 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 87 total
  • Cancer dependency (DepMap): dependent in 96.5% of screened cell lines (common-essential)
  • MANE Select transcript: NM_002484

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:8041
Approved symbolNUBP1
NameNUBP iron-sulfur cluster assembly factor 1, cytosolic
Location16p13.13
Locus typegene with protein product
StatusApproved
AliasesNBP35, CIAO5
Ensembl geneENSG00000103274
Ensembl biotypeprotein_coding
OMIM600280
Entrez4682

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 17 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000283027, ENST00000433392, ENST00000571175, ENST00000571790, ENST00000573663, ENST00000574137, ENST00000574334, ENST00000574691, ENST00000851530, ENST00000851531, ENST00000851532, ENST00000924644, ENST00000924645, ENST00000924646, ENST00000924647, ENST00000924648, ENST00000924649, ENST00000924650, ENST00000960378, ENST00000960379

RefSeq mRNA: 6 — MANE Select: NM_002484 NM_001278506, NM_001323594, NM_001323595, NM_001323596, NM_001323597, NM_002484

CCDS: CCDS10543, CCDS61839

Canonical transcript exons

ENST00000283027 — 11 exons

ExonStartEnd
ENSE000016484291074384210743882
ENSE000034731821074714310747276
ENSE000034984381076136410761474
ENSE000035124171076175710761859
ENSE000035195741076794910768032
ENSE000035444991076904710769351
ENSE000035540581075261010752678
ENSE000035784661075669010756780
ENSE000036308441075787310758027
ENSE000036374921074396110744065
ENSE000036395521075572110755753

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 94.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3834 / max 287.0956, expressed in 1818 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15270521.58261817
1527060.8007184

Top tissues by expression

285 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057694.04gold quality
mononuclear cellCL:000084293.47gold quality
right adrenal glandUBERON:000123393.41gold quality
leukocyteCL:000073893.39gold quality
apex of heartUBERON:000209893.32gold quality
left adrenal glandUBERON:000123493.20gold quality
left adrenal gland cortexUBERON:003582593.07gold quality
right adrenal gland cortexUBERON:003582792.86gold quality
heart left ventricleUBERON:000208492.80gold quality
right atrium auricular regionUBERON:000663192.66gold quality
granulocyteCL:000009492.50gold quality
cardiac ventricleUBERON:000208292.34gold quality
hindlimb stylopod muscleUBERON:000425291.71gold quality
olfactory segment of nasal mucosaUBERON:000538691.39gold quality
adrenal glandUBERON:000236991.25gold quality
body of pancreasUBERON:000115091.18gold quality
muscle of legUBERON:000138390.98gold quality
gastrocnemiusUBERON:000138890.92gold quality
heartUBERON:000094890.90gold quality
cardiac atriumUBERON:000208190.78gold quality
body of stomachUBERON:000116190.75gold quality
adrenal cortexUBERON:000123590.63gold quality
left uterine tubeUBERON:000130390.62gold quality
calcaneal tendonUBERON:000370190.43gold quality
muscle layer of sigmoid colonUBERON:003580590.37gold quality
lower esophagus muscularis layerUBERON:003583390.30gold quality
lower esophagusUBERON:001347390.28gold quality
esophagogastric junction muscularis propriaUBERON:003584189.96gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.68gold quality
left coronary arteryUBERON:000162689.68gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.48
E-GEOD-124858no52.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting NUBP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-7152-3P99.9767.47849
HSA-LET-7C-3P99.9573.422862
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-3177-5P99.6570.381174
HSA-MIR-425199.4069.193363
HSA-MIR-593-3P99.2267.281327
HSA-MIR-474499.0169.911581
HSA-MIR-392197.8167.451431
HSA-MIR-93897.4168.28656
HSA-MIR-4653-5P97.2267.721429
HSA-MIR-367497.0168.861171
HSA-MIR-6886-3P96.9666.36844
HSA-MIR-6734-5P95.7065.56950
HSA-MIR-10398-3P93.4663.6270

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • The cytosolic soluble P-loop NTPase termed huNbp35 (also known as Nubp1) was identified as an Fe/S protein, and its role in the maturation of Fe/S proteins in HeLa cells, is defined. (PMID:18573874)
  • GLRX3 Acts as a [2Fe-2S] Cluster Chaperone in the Cytosolic Iron-Sulfur Assembly Machinery Transferring [2Fe-2S] Clusters to NUBP1. (PMID:32429669)
  • Unraveling the mechanism of [4Fe-4S] cluster assembly on the N-terminal cluster binding site of NUBP1. (PMID:36916754)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionubp1ENSDARG00000055472
mus_musculusNubp1ENSMUSG00000022503
rattus_norvegicusNubp1ENSRNOG00000077863
drosophila_melanogasterNubp1FBGN0032597
caenorhabditis_elegansnubp-1WBGENE00008664

Paralogs (2): NUBP2 (ENSG00000095906), NUBPL (ENSG00000151413)

Protein

Protein identifiers

Cytosolic Fe-S cluster assembly factor NUBP1 — P53384 (reviewed: P53384)

Alternative names: Nucleotide-binding protein 1

All UniProt accessions (4): P53384, I3L3A0, I3L518, I3L531

UniProt curated annotations — full annotation on UniProt →

Function. Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. Required for maturation of extramitochondrial Fe-S proteins. The NUBP1-NUBP2 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins. Implicated in the regulation of centrosome duplication. Negatively regulates cilium formation and structure.

Subunit / interactions. Heterotetramer of 2 NUBP1 and 2 NUBP2 chains. Interacts with KIFC1. Interacts with NUBP2. Interacts with the BBS/CCT complex subunit CCT1.

Subcellular location. Cytoplasm. Nucleus. Cell projection. Cytoskeleton. Cilium axoneme. Cilium basal body. Microtubule organizing center. Centrosome. Centriole.

Cofactor. Binds 4 [4Fe-4S] clusters per heterotetramer. Contains two stable clusters in the N-termini of NUBP1 and two labile, bridging clusters between subunits of the NUBP1-NUBP2 heterotetramer.

Similarity. Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP1/NBP35 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
P53384-11yes
P53384-22

RefSeq proteins (6): NP_001265435, NP_001310523, NP_001310524, NP_001310525, NP_001310526, NP_002475* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000808Mrp-like_CSConserved_site
IPR003593AAA+_ATPaseDomain
IPR019591Mrp/NBP35_ATP-bdFamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR028601NUBP1/Nbp35Family
IPR033756YlxH/NBP35Family

Pfam: PF10609

UniProt features (14 total): binding site 7, sequence conflict 2, modified residue 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P53384-F190.000.70

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (7): 8; 22; 25; 31; 62–69; 235; 238

Post-translational modifications (2): 1, 319

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2564830Cytosolic iron-sulfur cluster assembly

MSigDB gene sets: 188 (showing top): GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_INTRACELLULAR_IRON_ION_HOMEOSTASIS, GOBP_GROWTH, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, MARTINEZ_RB1_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE, GOCC_CENTROSOME, GOBP_REGULATION_OF_CENTROSOME_CYCLE, PEART_HDAC_PROLIFERATION_CLUSTER_DN

GO Biological Process (7): regulation of cell growth (GO:0001558), intracellular iron ion homeostasis (GO:0006879), negative regulation of centrosome duplication (GO:0010826), iron-sulfur cluster assembly (GO:0016226), cell projection organization (GO:0030030), centrosome localization (GO:0051642), protein localization to cell cortex (GO:0072697)

GO Molecular Function (8): nucleotide binding (GO:0000166), ATP binding (GO:0005524), metal ion binding (GO:0046872), iron-sulfur cluster binding (GO:0051536), 4 iron, 4 sulfur cluster binding (GO:0051539), ATP-dependent FeS chaperone activity (GO:0140663), protein binding (GO:0005515), ATP hydrolysis activity (GO:0016887)

GO Cellular Component (14): nucleus (GO:0005634), Golgi apparatus (GO:0005794), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), axoneme (GO:0005930), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), sperm end piece (GO:0097229), cytoplasm (GO:0005737), microtubule organizing center (GO:0005815), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure8
sperm flagellum3
ATP-dependent activity2
intracellular membrane-bounded organelle2
cytoplasm2
microtubule organizing center2
intracellular membraneless organelle2
cell growth1
regulation of growth1
regulation of cellular component organization1
intracellular monoatomic cation homeostasis1
inorganic ion homeostasis1
regulation of centrosome duplication1
negative regulation of centrosome cycle1
centrosome duplication1
metallo-sulfur cluster assembly1
cellular component organization1
microtubule organizing center localization1
protein localization to cell periphery1
nucleoside phosphate binding1
heterocyclic compound binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
cation binding1
metal cluster binding1
iron-sulfur cluster binding1
metallochaperone activity1
binding1
ribonucleoside triphosphate phosphatase activity1
endomembrane system1
centriole1
cytoskeleton1
microtubule1
ciliary plasm1
intracellular anatomical structure1
microtubule cytoskeleton1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

1472 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NUBP1CIAO1O76071939
NUBP1CIAPIN1Q6FI81907
NUBP1CIAO3Q9H6Q4906
NUBP1MMS19Q96T76877
NUBP1FOXRED1Q96CU9829
NUBP1CIAO2BQ9Y3D0815
NUBP1ISCUQ9H1K1790
NUBP1NFS1Q9Y697780
NUBP1CIAO2AQ9H5X1773
NUBP1NDOR1Q9UHB4762
NUBP1LYRM4Q9HD34727
NUBP1NFU1Q9UMS0701
NUBP1ABCB7O75027696
NUBP1GLRX3O76003674
NUBP1IBA57Q5T440633

IntAct

13 interactions, top by confidence:

ABTypeScore
NUBP1NUBP2psi-mi:“MI:0915”(physical association)0.670
NUBP1psi-mi:“MI:0407”(direct interaction)0.560
SPRY2NUBP1psi-mi:“MI:0915”(physical association)0.370
Mpsi-mi:“MI:0914”(association)0.350
QPCTNUBP1psi-mi:“MI:0914”(association)0.350
NUBP1YBEYpsi-mi:“MI:0914”(association)0.350
NUBP2TK2psi-mi:“MI:0914”(association)0.350
CIAPIN1NUBP1psi-mi:“MI:0914”(association)0.350
CIAO3NUBP1psi-mi:“MI:0914”(association)0.350
NUBP2C1orf226psi-mi:“MI:0914”(association)0.350
HRASIGKV2D-24psi-mi:“MI:0914”(association)0.350

BioGRID (85): NUBP1 (Affinity Capture-MS), AIMP1 (Co-fractionation), NUBP1 (Two-hybrid), NUBP1 (Affinity Capture-MS), NUBP1 (Negative Genetic), NUBP1 (Negative Genetic), NUBP1 (Positive Genetic), NUBP1 (Positive Genetic), NUBP1 (Negative Genetic), NUBP1 (Negative Genetic), NUBP1 (Negative Genetic), NUBP1 (Negative Genetic), ORAOV1 (Negative Genetic), POLE (Negative Genetic), POLR3B (Positive Genetic)

ESM2 similar proteins: A1C7T4, A7RUD5, A8PW87, A8WWQ7, B0X4N8, B3MU92, B3NNJ9, B4G8R5, B4I540, B4IYG8, B4JBI7, B4KHX1, B4LGB4, B4LUF5, B4N1C3, B4P9A8, B4Q7F5, O94442, P0CO88, P0CO89, P52920, P53384, Q0CVD6, Q0UI56, Q16T79, Q1EAU8, Q24K00, Q29MT7, Q2H317, Q2UDE2, Q3KQF0, Q4HZ34, Q4WZS2, Q59MP1, Q5BBC5, Q5EB25, Q5I050, Q5I0L4, Q6BTZ6, Q6C7A6

Diamond homologs: A1C4X8, A1C7T4, A4QNM5, A7RUD5, A7SE07, A8PW87, A8WWQ7, A9V7A1, B0X4N8, B0XDJ0, B3M9R3, B3MU92, B3NIP2, B3NNJ9, B3RPX4, B4G8R5, B4H7P4, B4I540, B4IAD1, B4IUH5, B4IYG8, B4JBI7, B4KHX1, B4KY56, B4LGB4, B4LUF5, B4N1C3, B4N4D9, B4P9A8, B4PES4, B4Q7F5, B4QJ46, B6K1G6, O94442, P0C8Q1, P0CO88, P0CO89, P0CO90, P0CO91, P40558

SIGNOR signaling

1 interactions.

AEffectBMechanism
NUBP1“form complex”“NUBP1-NUBP2 iron-sulfur cluster assembly scaffold complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

87 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2162 predictions. Top by Δscore:

VariantEffectΔscore
16:10747138:TGCA:Tacceptor_loss1.0000
16:10747139:GCA:Gacceptor_loss1.0000
16:10747141:A:AGacceptor_gain1.0000
16:10747142:G:Aacceptor_loss1.0000
16:10747142:G:GGacceptor_gain1.0000
16:10747142:GCT:Gacceptor_gain1.0000
16:10747142:GCTAT:Gacceptor_gain1.0000
16:10757868:TCTA:Tacceptor_loss1.0000
16:10757871:A:AGacceptor_gain1.0000
16:10757871:AG:Aacceptor_gain1.0000
16:10757871:AGG:Aacceptor_loss1.0000
16:10757872:G:GTacceptor_gain1.0000
16:10757872:GG:Gacceptor_gain1.0000
16:10757872:GGC:Gacceptor_gain1.0000
16:10757872:GGCA:Gacceptor_gain1.0000
16:10757872:GGCAT:Gacceptor_gain1.0000
16:10758028:G:GAdonor_loss1.0000
16:10758028:G:GGdonor_gain1.0000
16:10761359:CGTA:Cacceptor_loss1.0000
16:10761360:GTAG:Gacceptor_loss1.0000
16:10761361:TA:Tacceptor_loss1.0000
16:10761362:A:AGacceptor_gain1.0000
16:10761362:A:ATacceptor_loss1.0000
16:10761362:AGGAG:Aacceptor_gain1.0000
16:10761363:G:GGacceptor_gain1.0000
16:10761363:GGA:Gacceptor_gain1.0000
16:10761363:GGAGG:Gacceptor_gain1.0000
16:10761472:AAG:Adonor_loss1.0000
16:10761474:GGTG:Gdonor_loss1.0000
16:10761475:G:Tdonor_loss1.0000

AlphaMissense

2106 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:10752629:A:TD93V0.999
16:10752630:T:AD93E0.999
16:10752630:T:GD93E0.999
16:10747221:A:TK68I0.998
16:10747223:A:CS69R0.998
16:10747225:C:AS69R0.998
16:10747225:C:GS69R0.998
16:10752629:A:CD93A0.998
16:10752632:T:AI94K0.998
16:10757905:T:AW162R0.998
16:10757905:T:CW162R0.998
16:10757924:T:CL168P0.998
16:10747206:A:TK63I0.997
16:10747218:G:AG67E0.997
16:10752620:T:CL90P0.997
16:10752622:G:CD91H0.997
16:10757907:G:CW162C0.997
16:10757907:G:TW162C0.997
16:10747217:G:AG67R0.996
16:10747217:G:CG67R0.996
16:10747217:G:TG67W0.996
16:10747220:A:CK68Q0.996
16:10747220:A:GK68E0.996
16:10747232:A:CS72R0.996
16:10747234:C:AS72R0.996
16:10747234:C:GS72R0.996
16:10747242:T:CL75P0.996
16:10752623:A:CD91A0.996
16:10752623:A:TD91V0.996
16:10752624:C:AD91E0.996

dbSNP variants (sampled 300 via entrez): RS1000043470 (16:10762721 A>G), RS1000092218 (16:10744769 T>A,G), RS1000173095 (16:10748203 G>A), RS1000186172 (16:10756971 T>C), RS1000338594 (16:10755098 A>G), RS1000432075 (16:10754777 G>A), RS1000498411 (16:10759843 C>G,T), RS1000556543 (16:10759595 A>G), RS1000625861 (16:10754333 C>T), RS1000780222 (16:10749179 G>A), RS1000907637 (16:10768907 G>A,C), RS1000953181 (16:10760163 T>A,C), RS1000986273 (16:10768159 G>A), RS1000990687 (16:10759749 C>T), RS1001157878 (16:10763506 C>G)

Disease associations

OMIM: gene MIM:600280 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007001_9Cerebrospinal AB1-42 levels in normal cognition5.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004670beta-amyloid 1-42 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
potassium chromate(VI)affects cotreatment, decreases expression, increases expression2
GSK-J4decreases expression1
FR900359increases phosphorylation1
trichostatin Aaffects expression1
4-aminophenylarsenoxideaffects binding, decreases reaction1
epigallocatechin gallateaffects cotreatment, decreases expression1
chromium hexavalent ionaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrineincreases expression1
LDN 193189affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Arsenic Trioxideaffects binding, decreases reaction1
Air Pollutantsaffects expression, increases abundance1
Cadmiumincreases abundance, increases expression1
Caffeineaffects phosphorylation1
Copperaffects binding, decreases expression1
Disulfiramaffects binding, decreases expression1
Ivermectindecreases expression1
Leadaffects expression1
Nickelincreases expression1
Ozoneaffects expression, increases abundance1
Plant Extractsaffects cotreatment, increases expression1
Smokedecreases expression1
Urethanedecreases expression1
Cadmium Chlorideincreases abundance, increases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

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