PSMD13 proteasome 26S subunit, non-ATPase 13 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PSMD13provided by HGNC
Official Full Name: proteasome 26S subunit, non-ATPase 13provided by HGNC
Primary source: HGNC:HGNC:9558
See related: Ensembl:ENSG00000185627 MIM:603481; AllianceGenome:HGNC:9558
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: S11; Rpn9; p40.5; HSPC027
Summary: 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]
Expression: Ubiquitous expression in appendix (RPKM 33.3), lymph node (RPKM 32.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.5

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (236976..252984)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (277982..293919)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (236976..252984)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk.
Title: Alternative splicing of PSMD13 mediated by genetic variants is significantly associated with endometrial cancer risk.
Data show that UBLCP1 selectively binds to the 26S proteasome non-ATPase regulatory subunit 13 (19S regulatory particle) in regulating proteasome assembly.
Title: Phosphatase UBLCP1 controls proteasome assembly.
Studies have found significant associations of the treatment response with the 26S proteasome non-ATPase subunit 9 (PSMD9), proteasome alpha type 7 subunit (PSMA7) and PSMD13 genes.
Title: Proteasome system dysregulation and treatment resistance mechanisms in major depressive disorder.
The SIRT3 5' flanking region encompasses the PSMD13 gene encoding the p40.5 regulator subunit of the 26S proteasome.
Title: Characterization of a bidirectional promoter shared between two human genes related to aging: SIRT3 and PSMD13.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. EBI GWAS Catalog EBI GWAS CatalogPubMed
New gene functions in megakaryopoiesis and platelet formation. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with PSMD13	PubMed
Tat	tat	Expression of HIV-1 Tat downregulates the abundance of proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 (PSMD13) in the nucleoli of Jurkat T-cells	PubMed
	tat	HIV-1 Tat slightly enhances the activity of the purified 26 S proteasome	PubMed
	tat	Amino acids Lys51, Arg52, and Asp67 of HIV-1 Tat represent the proteasome binding site of Tat, and Tat amino acids 37-72 are necessary for proteasomal interaction and suppression of 11 S regulator-mediated antigen presentation	PubMed
	tat	HIV-1 Tat inhibits the peptidase activity of the 20 S proteasome and interferes with the formation of the 20 S proteasome-11 S regulator complex	PubMed
	tat	HIV-1 Tat binds to the alpha2, alpha4, alpha6, alpha7, beta1, beta2, beta3, beta5, beta6, beta7, LMP7/beta5i, and MECL1/beta2i subunits of the proteasome 20 S core structure and can inhibit cellular proteasome function	PubMed
Vif	vif	HIV-1 Vif binds to the cellular cytidine deaminase APOBEC3G and targets it for degradation through an interaction with the proteasome, thereby inhibiting APOBEC3G mediated restriction of HIV-1 replication	PubMed
integrase	gag-pol	Proteasomal degradation of HIV-1 integrase in mammalian cells occurs by the N-end rule pathway	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2071 (e-PCR)
- UniSTS:150031

D15S1477 (e-PCR)
- UniSTS:474482

PSMD13_2898 (e-PCR)
- UniSTS:462469

STS-T99644 (e-PCR)
- UniSTS:62372

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in meiosis I	IEA Inferred from Electronic Annotation more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	NAS Non-traceable Author Statement more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in ficolin-1-rich granule lumen	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of proteasome accessory complex	ISS Inferred from Sequence or Structural Similarity more info
part_of proteasome complex	IDA Inferred from Direct Assay more info	PubMed
part_of proteasome complex	NAS Non-traceable Author Statement more info	PubMed
part_of proteasome regulatory particle	TAS Traceable Author Statement more info	PubMed
part_of proteasome regulatory particle, lid subcomplex	IBA Inferred from Biological aspect of Ancestor more info
located_in secretory granule lumen	TAS Traceable Author Statement more info

General protein information

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Preferred Names: 26S proteasome non-ATPase regulatory subunit 13

Names: 26S proteasome regulatory subunit RPN9; 26S proteasome regulatory subunit S11; 26S proteasome regulatory subunit p40.5; 26S proteasome subunit p40.5; proteasome (prosome, macropain) 26S subunit, non-ATPase, 13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_002817.4 → NP_002808.3 26S proteasome non-ATPase regulatory subunit 13 isoform 1

See identical proteins and their annotated locations for NP_002808.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AA931044, AB009398, AC136475

Consensus CDS

CCDS7692.1

UniProtKB/Swiss-Prot

B3KT15, O75831, Q53XU2, Q9UNM6, Q9UNV3

UniProtKB/TrEMBL

B2RBM7, Q53GN6

Related

ENSP00000436186.1, ENST00000532097.6

Conserved Domains (1) summary

pfam01399
Location:231 → 335

PCI; PCI domain
NM_175932.3 → NP_787128.2 26S proteasome non-ATPase regulatory subunit 13 isoform 2

See identical proteins and their annotated locations for NP_787128.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate segment and uses a different splice site in the 5' coding region, compared to variant 1. These differences cause a frameshift and then a restoration in the reading frame. Isoform 2 has a slightly shorter N-terminus, compared to isoform 1.

Source sequence(s)

AA931044, AC136475, AK094775, AL556906

Consensus CDS

CCDS44504.1

UniProtKB/TrEMBL

B2RBM7

Related

ENSP00000396937.2, ENST00000431206.6

Conserved Domains (1) summary

pfam01399
Location:233 → 337

PCI; PCI domain