PSMD5

gene
On this page

Also known as S5BKIAA0072

Summary

PSMD5 (proteasome 26S subunit, non-ATPase 5, HGNC:9563) is a protein-coding gene on chromosome 9q33.2, encoding 26S proteasome non-ATPase regulatory subunit 5 (Q16401). Acts as a chaperone during the assembly of the 26S proteasome, specifically of the base subcomplex of the PA700/19S regulatory complex (RC).

The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. This gene encodes a non-ATPase subunit of the 19S regulator base that functions as a chaperone protein during 26S proteasome assembly.

Source: NCBI Gene 5711 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 75 total
  • Druggable target: yes
  • MANE Select transcript: NM_005047

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9563
Approved symbolPSMD5
Nameproteasome 26S subunit, non-ATPase 5
Location9q33.2
Locus typegene with protein product
StatusApproved
AliasesS5B, KIAA0072
Ensembl geneENSG00000095261
Ensembl biotypeprotein_coding
OMIM604452
Entrez5711

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000210313, ENST00000373903, ENST00000373904, ENST00000373920, ENST00000471789, ENST00000476949, ENST00000496688, ENST00000625444, ENST00000899083, ENST00000963400

RefSeq mRNA: 2 — MANE Select: NM_005047 NM_001270427, NM_005047

CCDS: CCDS59143, CCDS6824

Canonical transcript exons

ENST00000210313 — 10 exons

ExonStartEnd
ENSE00001656052120829099120829208
ENSE00001664782120826765120826907
ENSE00001680614120821355120821464
ENSE00001714724120820839120820979
ENSE00001724122120824494120824685
ENSE00001749259120831331120831459
ENSE00001853489120816053120818163
ENSE00001896328120842737120842922
ENSE00003466325120833312120833456
ENSE00003648374120831832120831945

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 94.26.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.0077 / max 165.8884, expressed in 1780 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
10230411.00771780

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
hair follicleUBERON:000207394.26gold quality
esophagus squamous epitheliumUBERON:000692092.39gold quality
tongue squamous epitheliumUBERON:000691991.84gold quality
tibiaUBERON:000097991.72gold quality
epithelium of esophagusUBERON:000197691.51gold quality
squamous epitheliumUBERON:000691490.30gold quality
epithelium of mammary glandUBERON:000324489.44gold quality
mammary ductUBERON:000176589.07gold quality
islet of LangerhansUBERON:000000689.03gold quality
calcaneal tendonUBERON:000370189.03gold quality
oviduct epitheliumUBERON:000480489.03gold quality
secondary oocyteCL:000065588.95gold quality
periodontal ligamentUBERON:000826688.91gold quality
lower lobe of lungUBERON:000894988.89gold quality
gingivaUBERON:000182888.77gold quality
thoracic mammary glandUBERON:000520088.57gold quality
mammary glandUBERON:000191188.54gold quality
upper arm skinUBERON:000426388.54gold quality
right adrenal glandUBERON:000123388.51gold quality
palpebral conjunctivaUBERON:000181288.47gold quality
left adrenal glandUBERON:000123488.37gold quality
gingival epitheliumUBERON:000194988.35gold quality
endometriumUBERON:000129588.33gold quality
cauda epididymisUBERON:000436088.33gold quality
adrenal glandUBERON:000236988.29gold quality
upper leg skinUBERON:000426288.18gold quality
parietal pleuraUBERON:000240088.17gold quality
descending thoracic aortaUBERON:000234588.16gold quality
right adrenal gland cortexUBERON:003582788.16gold quality
deciduaUBERON:000245087.93gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

85 targeting PSMD5, 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-3646100.0073.565283
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5692A100.0074.406850
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-569699.9872.364487
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-1213699.9872.815713
HSA-MIR-56899.9869.862084
HSA-MIR-548N99.9871.944170
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-314899.9775.066478
HSA-MIR-211099.9666.681930
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-590-3P99.9674.346478
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-545-3P99.9570.742783
HSA-LET-7C-3P99.9573.422862
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-311999.9271.342390
HSA-MIR-380-3P99.8970.181978
HSA-MIR-153-5P99.8973.866317
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-990299.8969.152250
HSA-MIR-4524A-3P99.7266.852406

Literature-anchored findings (GeneRIF, showing 2)

  • the critical role of S5b/PSMD5 in negative regulation of proteasome by TNF-alpha/NFkappaB and provide insights into proteasome inhibition in human disease. (PMID:22921402)
  • Study in HT-29 cells and mouse colorectal tumor models revealed that levels of the proteasome assembly inhibitor PSMD5/S5B are significantly decreased in tumors, and re-expression of PSMD5 blocks 26S proteasome assembly. These results suggest that intestinal cancer cells escape proteotoxic stress by reducing PSMD5 to stimulate 26S proteasome assembly. (PMID:29716915)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopsmd5ENSDARG00000059046
mus_musculusPsmd5ENSMUSG00000026869
rattus_norvegicusPsmd5ENSRNOG00000018809
drosophila_melanogasterCG12096FBGN0030457
caenorhabditis_elegansWBGENE00009445

Protein

Protein identifiers

26S proteasome non-ATPase regulatory subunit 5Q16401 (reviewed: Q16401)

Alternative names: 26S protease subunit S5 basic, 26S proteasome subunit S5B

All UniProt accessions (3): Q16401, F2Z3J2, Q4VXH0

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a chaperone during the assembly of the 26S proteasome, specifically of the base subcomplex of the PA700/19S regulatory complex (RC). In the initial step of the base subcomplex assembly is part of an intermediate PSMD5:PSMC2:PSMC1:PSMD2 module which probably assembles with a PSMD10:PSMC4:PSMC5:PAAF1 module followed by dissociation of PSMD5.

Subunit / interactions. Interacts with PSMC1, PSMC2, PSMD1 and PSMD6. Part of transient complex containing PSMD5, PSMC2, PSMC1 and PSMD2 formed during the assembly of the 26S proteasome.

Domain organisation. Rich in dileucine repeats, which have been implicated in trafficking of a variety of transmembrane proteins.

Similarity. Belongs to the proteasome subunit S5B/HSM3 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q16401-11yes
Q16401-22

RefSeq proteins (2): NP_001257356, NP_005038* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011989ARM-likeHomologous_superfamily
IPR016024ARM-type_foldHomologous_superfamily
IPR019538PSMD5Family

Pfam: PF10508

UniProt features (6 total): sequence variant 2, initiator methionine 1, chain 1, modified residue 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16401-F193.960.89

Functional residue map

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

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9907900Proteasome assembly

MSigDB gene sets: 114 (showing top): GOBP_PROTEASOME_ASSEMBLY, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, WANG_LMO4_TARGETS_DN, DOUGLAS_BMI1_TARGETS_DN, DANG_BOUND_BY_MYC, GOCC_PROTEASOME_REGULATORY_PARTICLE_BASE_SUBCOMPLEX, MARSON_BOUND_BY_FOXP3_STIMULATED, BENPORATH_MYC_MAX_TARGETS, GOCC_PROTEASOME_ACCESSORY_COMPLEX, SWEET_LUNG_CANCER_KRAS_UP, CHENG_RESPONSE_TO_NICKEL_ACETATE, REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, LINDGREN_BLADDER_CANCER_CLUSTER_1_UP, LEE_BMP2_TARGETS_DN, GOCC_PEPTIDASE_COMPLEX

GO Biological Process (2): proteasome regulatory particle assembly (GO:0070682), proteasome assembly (GO:0043248)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): proteasome complex (GO:0000502), cytosol (GO:0005829), proteasome accessory complex (GO:0022624), proteasome regulatory particle, base subcomplex (GO:0008540)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein-containing complex2
proteasome assembly1
protein-containing complex assembly1
binding1
intracellular protein-containing complex1
endopeptidase complex1
cytoplasm1
cellular anatomical structure1
proteasome complex1
intracellular anatomical structure1
proteasome regulatory particle1

Protein interactions and networks

STRING

1260 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PSMD5PSMD4P55036976
PSMD5PSMC1P49014816
PSMD5PSMD2Q13200793
PSMD5PSMD7P51665779
PSMD5PSMD11O00231770
PSMD5LONP1P36776747
PSMD5ADRM1Q16186746
PSMD5PSMD1Q99460702
PSMD5PSMC6P49719684
PSMD5PSMD9O00233679
PSMD5PSMD8P48556671
PSMD5PSMD6Q15008665
PSMD5PSMC4P43686626
PSMD5UCHL5Q9Y5K5625
PSMD5PSMC3P17980605

IntAct

112 interactions, top by confidence:

ABTypeScore
PSMD5PSMC2psi-mi:“MI:0915”(physical association)0.960
PSMC2PSMD5psi-mi:“MI:0915”(physical association)0.960
PSMD5PSMC2psi-mi:“MI:0914”(association)0.960
PSMD5PSMC2psi-mi:“MI:0407”(direct interaction)0.960
PSMC1PSMD5psi-mi:“MI:0915”(physical association)0.940
PSMD5PSMC1psi-mi:“MI:0915”(physical association)0.940
PSMC3PSMD9psi-mi:“MI:0914”(association)0.940
KIFAP3KIF3Bpsi-mi:“MI:0914”(association)0.900
PSMC1PSMC2psi-mi:“MI:0914”(association)0.890
UCHL5PSMD12psi-mi:“MI:0914”(association)0.840
PSMD10PSMD11psi-mi:“MI:0914”(association)0.800
PSMD13PSMD11psi-mi:“MI:0914”(association)0.750
PSMD4PSMD11psi-mi:“MI:0914”(association)0.750
PSMD7PSMD11psi-mi:“MI:0914”(association)0.730
PSMC5PSMD11psi-mi:“MI:0914”(association)0.730

BioGRID (269): PSMD5 (Two-hybrid), PSMD5 (Two-hybrid), TFCP2 (Two-hybrid), PSMD5 (Two-hybrid), BAG1 (Co-fractionation), DIS3L2 (Co-fractionation), GCSH (Co-fractionation), LAMB1 (Co-fractionation), MCM3 (Co-fractionation), P4HA1 (Co-fractionation), PAAF1 (Co-fractionation), PFKL (Co-fractionation), PFKM (Co-fractionation), PSMA3 (Co-fractionation), PSMA4 (Co-fractionation)

ESM2 similar proteins: A0JMW2, A2VE70, A5WW24, A7E2Y6, B9EJR8, E0CZ22, E1BP36, E7FBU4, O35638, O43156, O70576, O75155, Q08AM6, Q0P5A6, Q0V9L1, Q16401, Q5IFJ8, Q5JTH9, Q5R6L5, Q5ZIW5, Q5ZKD5, Q66L58, Q68F38, Q6DCF2, Q6P5B0, Q6ZQ73, Q7TMY7, Q80W92, Q80WQ2, Q84ZC0, Q86Y56, Q8C0Y0, Q8K2V6, Q8NDA8, Q8WVM7, Q91V83, Q96T76, Q99M76, Q9BPX3, Q9D071

Diamond homologs: Q0P5A6, Q16401, Q5IFJ8, Q8BJY1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Autodegradation of the E3 ubiquitin ligase COP11465.2×1e-20
Regulation of activated PAK-2p34 by proteasome mediated degradation1363.5×6e-19
Regulation of ornithine decarboxylase (ODC)1362.0×6e-19
Vpu mediated degradation of CD41360.6×6e-19
Ubiquitin-dependent degradation of Cyclin D1360.6×6e-19
Cross-presentation of soluble exogenous antigens (endosomes)1357.9×8e-19
Vif-mediated degradation of APOBEC3G1357.9×8e-19
Proteasome assembly1657.2×2e-22

GO biological processes:

GO termPartnersFoldFDR
proteasome-mediated ubiquitin-dependent protein catabolic process1611.8×2e-10

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance59
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1241 predictions. Top by Δscore:

VariantEffectΔscore
9:120820976:CAGG:Cacceptor_gain1.0000
9:120820978:GG:Gacceptor_gain1.0000
9:120820978:GGCTA:Gacceptor_loss1.0000
9:120820979:GCTA:Gacceptor_loss1.0000
9:120820980:C:CCacceptor_gain1.0000
9:120820980:C:CGacceptor_loss1.0000
9:120829205:TTAG:Tacceptor_gain1.0000
9:120831461:T:Cacceptor_gain1.0000
9:120831831:CCG:Cdonor_gain1.0000
9:120820834:CCT:Cdonor_loss0.9900
9:120820835:CT:Cdonor_loss0.9900
9:120820836:TA:Tdonor_loss0.9900
9:120820838:C:CTdonor_loss0.9900
9:120820975:TCAGG:Tacceptor_gain0.9900
9:120820976:CAGGC:Cacceptor_gain0.9900
9:120820977:AGG:Aacceptor_gain0.9900
9:120820983:C:CTacceptor_gain0.9900
9:120820984:A:Tacceptor_gain0.9900
9:120826908:C:CCacceptor_gain0.9900
9:120829111:T:TAdonor_gain0.9900
9:120829204:ATTAG:Aacceptor_gain0.9900
9:120829206:TAG:Tacceptor_gain0.9900
9:120829208:GC:Gacceptor_loss0.9900
9:120829209:C:Aacceptor_loss0.9900
9:120829209:C:CCacceptor_gain0.9900
9:120829214:A:ACacceptor_gain0.9900
9:120831324:ATCTT:Adonor_loss0.9900
9:120831325:TCTTA:Tdonor_loss0.9900
9:120831326:CTTAC:Cdonor_loss0.9900
9:120831327:TTACC:Tdonor_loss0.9900

AlphaMissense

3256 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:120817959:C:GG488R0.996
9:120817959:C:TG488R0.996
9:120818145:A:GW426R0.996
9:120818145:A:TW426R0.996
9:120817958:C:TG488E0.995
9:120817959:C:AG488W0.995
9:120817979:A:GL481P0.995
9:120818033:A:GL463P0.993
9:120818045:A:GL459P0.993
9:120820937:A:GW387R0.993
9:120820937:A:TW387R0.993
9:120824518:C:GG328R0.993
9:120824518:C:TG328R0.993
9:120829207:A:GL188P0.993
9:120824532:C:TG323E0.992
9:120824533:C:GG323R0.992
9:120824533:C:TG323R0.992
9:120824556:G:TA315D0.992
9:120824661:A:GL280P0.992
9:120818053:T:AK456N0.991
9:120818053:T:GK456N0.991
9:120826848:A:GL244P0.991
9:120831347:C:GR182P0.991
9:120831459:C:GA145P0.989
9:120817958:C:AG488V0.988
9:120818143:C:AW426C0.988
9:120818143:C:GW426C0.988
9:120824547:G:TT318K0.988
9:120818156:G:TA422E0.987
9:120829112:C:GD220H0.987

dbSNP variants (sampled 300 via entrez): RS1000017057 (9:120826175 T>A), RS1000269805 (9:120818127 AC>A), RS1000390465 (9:120843569 G>A,C,T), RS1000419449 (9:120837451 C>T), RS1000534873 (9:120833104 T>A), RS1000591856 (9:120830030 G>A), RS1000731406 (9:120837496 C>A,T), RS1000787020 (9:120838950 A>T), RS1000825402 (9:120816503 G>A), RS1000996779 (9:120824303 C>A,T), RS1001054704 (9:120832343 G>C), RS1001075924 (9:120824119 A>AG), RS1001098222 (9:120825256 A>T), RS1001276257 (9:120817705 T>G), RS1001429870 (9:120826830 A>G)

Disease associations

OMIM: gene MIM:604452 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006259_41Systolic blood pressure6.000000e-10
GCST90020028_393Hip circumference adjusted for BMI6.000000e-09
GCST90020028_394Hip circumference adjusted for BMI2.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0006335systolic blood pressure
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067067 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.31Kd0.486nMCHEMBL5653589
9.31ED500.486nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2149128: Binding affinity to human PSMD5 incubated for 45 mins by Kinobead based pull down assaykd0.0005uM

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases expression, affects expression3
Cadmium Chloridedecreases expression, increases expression2
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression1
cobaltous chlorideincreases expression1
1-nitropyreneincreases expression1
di-n-butylphosphoric acidaffects expression1
nickel acetateaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
nutlin 3affects cotreatment, increases secretion1
LDN 193189decreases expression, affects cotreatment1
bisphenol AFincreases expression1
Sunitinibincreases expression1
Acetaminophendecreases expression1
Dactinomycinaffects cotreatment, increases secretion1
Dinitrochlorobenzeneaffects binding1
Doxorubicindecreases expression1
Ivermectindecreases expression1
Ketoconazoleincreases expression1
Leadaffects expression1
Quercetindecreases expression1
Testosteronedecreases expression1
Urethanedecreases expression1
Valproic Acidaffects expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652170BindingBinding affinity to human PSMD5 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2CHAbcam HeLa PSMD5 KOCancer cell lineFemale

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.