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

Gene ID: 5719, updated on 6-Sep-2020

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
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

Genomic context

See PSMD13 in Genome Data Viewer
Location:
11p15.5
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (236972..252984)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (236808..252984)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene microRNA 6743 Neighboring gene RIC8 guanine nucleotide exchange factor A Neighboring gene sirtuin 3 Neighboring gene signal recognition particle 19kDa pseudogene Neighboring gene cytochrome c oxidase subunit 8B, pseudogene Neighboring gene NLR family pyrin domain containing 6

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Phenotypes

Associated conditions

Description Tests
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
GeneReviews: Not available
New gene functions in megakaryopoiesis and platelet formation.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
structural molecule activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
Fc-epsilon receptor signaling pathway TAS
Traceable Author Statement
more info
 
MAPK cascade TAS
Traceable Author Statement
more info
 
NIK/NF-kappaB signaling TAS
Traceable Author Statement
more info
 
SCF-dependent proteasomal ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 
T cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
Wnt signaling pathway, planar cell polarity pathway TAS
Traceable Author Statement
more info
 
anaphase-promoting complex-dependent catabolic process TAS
Traceable Author Statement
more info
 
antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS
Traceable Author Statement
more info
 
interleukin-1-mediated signaling pathway TAS
Traceable Author Statement
more info
 
meiosis I IEA
Inferred from Electronic Annotation
more info
 
negative regulation of G2/M transition of mitotic cell cycle TAS
Traceable Author Statement
more info
 
negative regulation of canonical Wnt signaling pathway TAS
Traceable Author Statement
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of canonical Wnt signaling pathway TAS
Traceable Author Statement
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
proteasome assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein polyubiquitination TAS
Traceable Author Statement
more info
 
regulation of cellular amino acid metabolic process TAS
Traceable Author Statement
more info
 
regulation of hematopoietic stem cell differentiation TAS
Traceable Author Statement
more info
 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
regulation of mitotic cell cycle phase transition TAS
Traceable Author Statement
more info
 
regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
Traceable Author Statement
more info
 
stimulatory C-type lectin receptor signaling pathway TAS
Traceable Author Statement
more info
 
transmembrane transport TAS
Traceable Author Statement
more info
 
tumor necrosis factor-mediated signaling pathway TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
membrane HDA PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome accessory complex ISS
Inferred from Sequence or Structural Similarity
more info
 
proteasome complex IDA
Inferred from Direct Assay
more info
PubMed 
proteasome regulatory particle TAS
Traceable Author Statement
more info
PubMed 
proteasome regulatory particle, lid subcomplex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
secretory granule lumen TAS
Traceable Author Statement
more info
 

General protein information

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)

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)

  1. NM_002817.4NP_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
    Q9UNM6
    Related
    ENSP00000436186.1, ENST00000532097.6
    Conserved Domains (1) summary
    pfam01399
    Location:231335
    PCI; PCI domain
  2. NM_175932.3NP_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/Swiss-Prot
    Q9UNM6
    Related
    ENSP00000396937.2, ENST00000431206.6
    Conserved Domains (1) summary
    pfam01399
    Location:233337
    PCI; PCI domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    236972..252984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520235.3XP_011518537.1  26S proteasome non-ATPase regulatory subunit 13 isoform X1

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