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 n... See more...

Aliases for PSMD13 Gene

Aliases for PSMD13 Gene

  • Proteasome 26S Subunit, Non-ATPase 13 2 3 5
  • Proteasome (Prosome, Macropain) 26S Subunit, Non-ATPase, 13 2 3
  • 26S Proteasome Non-ATPase Regulatory Subunit 13 3 4
  • 26S Proteasome Regulatory Subunit P40.5 3 4
  • 26S Proteasome Regulatory Subunit RPN9 3 4
  • 26S Proteasome Regulatory Subunit S11 3 4
  • P40.5 2 3
  • Rpn9 2 3
  • 26S Proteasome Subunit P40.5 3
  • HSPC027 3
  • PSMD13 5
  • S11 3

External Ids for PSMD13 Gene

Previous GeneCards Identifiers for PSMD13 Gene

  • GC11P000459
  • GC11P000281
  • GC11M000945
  • GC11P000226
  • GC11P000056

Summaries for PSMD13 Gene

Entrez Gene Summary for PSMD13 Gene

  • 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. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for PSMD13 Gene

PSMD13 (Proteasome 26S Subunit, Non-ATPase 13) is a Protein Coding gene. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and Antigen processing-Cross presentation.

UniProtKB/Swiss-Prot Summary for PSMD13 Gene

  • Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair.

Gene Wiki entry for PSMD13 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PSMD13 Gene

Genomics for PSMD13 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PSMD13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J000234 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 644.3 -0.3 -274 3.8 SP1 HNRNPL CREB1 GATAD2A PRDM10 TFE3 RFX1 LEF1 ZNF692 POLR2A PSMD13 HSALNG0081942 SIRT3 RIC8A BET1L SNORA52 RNH1 GATD1 TMEM80 ENSG00000255237
GH11J000205 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 32.6 -28.3 -28254 6 SP1 CREB1 GATAD2A ZBTB33 HNRNPL PRDM10 REST ZNF629 ZNF512 IKZF1 BET1L RIC8A MIR6743 lnc-SIRT3-1 lnc-RIC8A-2 PSMD13 TMEM80 SNORA52 ENSG00000255237 TSPAN4
GH11J000266 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 24.7 +33.1 33086 6.8 SP1 LEF1 POLR2A BACH1 JUND LARP7 STAT3 DDX20 ZNF143 MTA2 IFITM2 PSMD13 RIC8A SIRT3 PGGHG ENSG00000254559 ODF3 SCGB1C1 BET1L NLRP6
GH11J000222 Enhancer 1.1 Ensembl ENCODE dbSUPER 29.8 -15.2 -15236 1.1 IKZF1 HDAC1 FOXJ2 GTF2E2 ZNF766 HMBOX1 MTA3 E2F5 NR2C2 ZBTB11 RIC8A PSMD13 SIRT3 ODF3 SCGB1C1 BET1L NLRP6 PGGHG ENSG00000255026 piR-43105-065
GH11J000201 Promoter/Enhancer 0.7 Ensembl ENCODE 32.3 -34.8 -34771 1.1 SPI1 SUPT5H POLR2A ENSG00000254559 piR-37158 PSMD13 SIRT3 BET1L ODF3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PSMD13 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PSMD13

Top Transcription factor binding sites by QIAGEN in the PSMD13 gene promoter:
  • aMEF-2
  • Arnt
  • COMP1
  • HTF
  • MEF-2
  • MEF-2A
  • Olf-1
  • Pax-2
  • Pax-2a
  • RREB-1

Genomic Locations for PSMD13 Gene

Genomic Locations for PSMD13 Gene
chr11:236,966-252,984
(GRCh38/hg38)
Size:
16,019 bases
Orientation:
Plus strand
chr11:236,546-252,984
(GRCh37/hg19)
Size:
16,439 bases
Orientation:
Plus strand

Genomic View for PSMD13 Gene

Genes around PSMD13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PSMD13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PSMD13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PSMD13 Gene

Proteins for PSMD13 Gene

  • Protein details for PSMD13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UNM6-PSD13_HUMAN
    Recommended name:
    26S proteasome non-ATPase regulatory subunit 13
    Protein Accession:
    Q9UNM6
    Secondary Accessions:
    • B3KT15
    • O75831
    • Q53XU2
    • Q9UNV3

    Protein attributes for PSMD13 Gene

    Size:
    376 amino acids
    Molecular mass:
    42945 Da
    Quaternary structure:
    • Component of the 19S proteasome regulatory particle complex. The 26S proteasome consists of a 20S core particle (CP) and two 19S regulatory subunits (RP). The regulatory particle is made of a lid composed of 9 subunits including PSMD13, a base containing 6 ATPases and few additional components.

    Three dimensional structures from OCA and Proteopedia for PSMD13 Gene

    Alternative splice isoforms for PSMD13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PSMD13 Gene

Post-translational modifications for PSMD13 Gene

  • Ubiquitination at Lys2, Lys99, Lys115, Lys122, Lys161, Lys174, Lys186, Lys252, Lys313, Lys321, and Lys347
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PSMD13 Gene

Domains & Families for PSMD13 Gene

Gene Families for PSMD13 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PSMD13 Gene

InterPro:
Blocks:
  • Domain in components of the proteasome, COP9-complex and eIF3 (PCI)
ProtoNet:

Suggested Antigen Peptide Sequences for PSMD13 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53046, highly similar to 26S proteasome non-ATPase regulatory subunit 13 (B4DJ66_HUMAN)
  • 26S proteasome regulatory subunit p40.5 (PSD13_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UNM6

UniProtKB/Swiss-Prot:

PSD13_HUMAN :
  • Belongs to the proteasome subunit S11 family.
Family:
  • Belongs to the proteasome subunit S11 family.
genes like me logo Genes that share domains with PSMD13: view

Function for PSMD13 Gene

Molecular function for PSMD13 Gene

UniProtKB/Swiss-Prot Function:
Component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. This complex plays a key role in the maintenance of protein homeostasis by removing misfolded or damaged proteins, which could impair cellular functions, and by removing proteins whose functions are no longer required. Therefore, the proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair.

Phenotypes From GWAS Catalog for PSMD13 Gene

Gene Ontology (GO) - Molecular Function for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005198 structural molecule activity IBA 21873635
genes like me logo Genes that share ontologies with PSMD13: view
genes like me logo Genes that share phenotypes with PSMD13: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PSMD13

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PSMD13 Gene

Localization for PSMD13 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PSMD13 gene
Compartment Confidence
nucleus 5
extracellular 4
cytosol 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000502 proteasome complex TAS,IDA 17323924
GO:0005576 extracellular region TAS --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PSMD13: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PSMD13 Gene

Pathways & Interactions for PSMD13 Gene

PathCards logo

SuperPathways for PSMD13 Gene

SuperPathway Contained pathways
1 Regulation of activated PAK-2p34 by proteasome mediated degradation
.78
2 RET signaling
3 HIV Life Cycle
.45
4 Parkinson disease
5 Class I MHC mediated antigen processing and presentation
genes like me logo Genes that share pathways with PSMD13: view

Pathways by source for PSMD13 Gene

3 GeneGo (Thomson Reuters) pathways for PSMD13 Gene
  • Immune response Antigen presentation by MHC class I
  • Proteolysis Role of Parkin in the Ubiquitin-Proteasomal Pathway
  • Transcription Ligand-Dependent Transcription of Retinoid-Target genes
2 Qiagen pathways for PSMD13 Gene
  • RAR-Gamma-RXR-Alpha Degradation
  • Remodeling of Adherens Junctions

Gene Ontology (GO) - Biological Process for PSMD13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade TAS --
GO:0000209 protein polyubiquitination TAS --
GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS --
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS --
GO:0006511 ubiquitin-dependent protein catabolic process IBA 21873635
genes like me logo Genes that share ontologies with PSMD13: view

No data available for SIGNOR curated interactions for PSMD13 Gene

Drugs & Compounds for PSMD13 Gene

(2) Drugs for PSMD13 Gene - From: DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bortezomib Approved, Investigational Pharma inhibitor, other Proteosome and NF-kappaB inhibitor, Other, Proteasome inhibitors 910
carfilzomib Approved, Investigational Pharma other, Inhibitor Other, 20S Proteasome Inhibitor 0
genes like me logo Genes that share compounds with PSMD13: view

Transcripts for PSMD13 Gene

mRNA/cDNA for PSMD13 Gene

2 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PSMD13

Alternative Splicing Database (ASD) splice patterns (SP) for PSMD13 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b · 14c · 14d
SP1: - - -
SP2: - - - -
SP3: - -
SP4: -
SP5: - - - -
SP6:
SP7:
SP8:

Relevant External Links for PSMD13 Gene

GeneLoc Exon Structure for
PSMD13

Expression for PSMD13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PSMD13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PSMD13 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PSMD13 Gene



Protein tissue co-expression partners for PSMD13 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PSMD13

SOURCE GeneReport for Unigene cluster for PSMD13 Gene:

Hs.134688

Evidence on tissue expression from TISSUES for PSMD13 Gene

  • Nervous system(4.9)
  • Lung(4.7)
  • Liver(4.5)
  • Blood(4.5)
  • Kidney(4.5)
  • Skin(4.1)
  • Intestine(2.7)
  • Eye(2.7)
  • Muscle(2.5)
  • Adrenal gland(2.4)
  • Pancreas(2.3)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with PSMD13: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PSMD13 Gene

Orthologs for PSMD13 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PSMD13 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PSMD13 30 31
  • 99.56 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PSMD13 30 31
  • 92.82 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PSMD13 30 31
  • 91.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Psmd13 30
  • 90.07 (n)
Mouse
(Mus musculus)
Mammalia Psmd13 30 17 31
  • 89.98 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PSMD13 31
  • 51 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PSMD13 31
  • 50 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PSMD13 30 31
  • 82.89 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 85 (a)
OneToMany
-- 31
  • 84 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia psmd13 30
  • 76.06 (n)
Str.1435 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.3428 30
Zebrafish
(Danio rerio)
Actinopterygii psmd13 30 31
  • 73.67 (n)
OneToOne
zgc56377 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9211 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001651 30
  • 55.14 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Rpn9 30 31 32
  • 52.99 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea rpn-9 30 31
  • 48.92 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPN9 30 31 33 33
  • 44.85 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B00825g 30
  • 44.83 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADR191C 30
  • 44.13 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G19006 30
  • 51.8 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0511300 30
  • 50.27 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 59 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU02374 30
  • 51.54 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rpn9 30
  • 45.76 (n)
Species where no ortholog for PSMD13 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PSMD13 Gene

ENSEMBL:
Gene Tree for PSMD13 (if available)
TreeFam:
Gene Tree for PSMD13 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PSMD13: view image

Paralogs for PSMD13 Gene

(1) SIMAP similar genes for PSMD13 Gene using alignment to 8 proteins:

  • PSD13_HUMAN
  • B4DJ66_HUMAN
  • E9PL38_HUMAN
  • E9PPD2_HUMAN
  • E9PQG3_HUMAN
  • F8W8J6_HUMAN
  • H0YD73_HUMAN
  • J3KNQ3_HUMAN
genes like me logo Genes that share paralogs with PSMD13: view

No data available for Paralogs for PSMD13 Gene

Variants for PSMD13 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PSMD13 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs1045288 - p.Asn13Ser
rs1794108 - p.Gly204Glu
rs1794109 - p.Leu205Phe
rs28927679 - p.Ser150Leu

Additional dbSNP identifiers (rs#s) for PSMD13 Gene

Structural Variations from Database of Genomic Variants (DGV) for PSMD13 Gene

Variant ID Type Subtype PubMed ID
dgv1010n100 CNV gain 25217958
dgv1011n100 CNV gain 25217958
dgv1012n100 CNV gain 25217958
dgv1505n54 CNV gain 21841781
esv32593 CNV loss 17666407
esv3625060 CNV gain 21293372
esv3625064 CNV gain 21293372
nsv1052484 CNV gain 25217958
nsv1069987 CNV deletion 25765185
nsv467631 CNV gain 19166990
nsv469921 CNV gain 18288195
nsv516439 CNV loss 19592680
nsv522596 CNV gain 19592680
nsv527533 CNV gain 19592680
nsv552762 CNV gain 21841781
nsv552765 CNV gain 21841781
nsv552766 CNV loss 21841781
nsv552767 CNV loss 21841781
nsv7632 CNV insertion 18451855

Variation tolerance for PSMD13 Gene

Residual Variation Intolerance Score: 53% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.46; 28.56% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PSMD13 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PSMD13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PSMD13 Gene

Disorders for PSMD13 Gene

No disorders were found for PSMD13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PSMD13 Gene

Publications for PSMD13 Gene

  1. cDNA cloning and functional analysis of p28 (Nas6p) and p40.5 (Nas7p), two novel regulatory subunits of the 26S proteasome. (PMID: 9714768) Hori T … Tanaka K (Gene 1998) 2 3 4 23
  2. An atomic structure of the human 26S proteasome. (PMID: 27428775) Huang X … Shi Y (Nature structural & molecular biology 2016) 3 4
  3. Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. (PMID: 17323924) Wang X … Huang L (Biochemistry 2007) 3 4
  4. Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13. (PMID: 17059877) Bellizzi D … De Benedictis G (Genomics 2007) 3 23
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for PSMD13 Gene