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

Gene ID: 5719, updated on 27-Nov-2024

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
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Genomic context

See PSMD13 in Genome Data Viewer
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_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:208989-209576 Neighboring gene microRNA 6743 Neighboring gene RIC8 guanine nucleotide exchange factor A Neighboring gene sirtuin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4256 Neighboring gene signal recognition particle 19kDa pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:257568-258068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2990 Neighboring gene cytochrome c oxidase subunit 8B, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4257 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:279707-280257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:283867-284636 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

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
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

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

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 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus HDA 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

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)

  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
    B3KT15, O75831, Q53XU2, Q9UNM6, Q9UNV3
    UniProtKB/TrEMBL
    B2RBM7, Q53GN6
    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/TrEMBL
    B2RBM7
    Related
    ENSP00000396937.2, ENST00000431206.6
    Conserved Domains (1) summary
    pfam01399
    Location:233337
    PCI; PCI domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    236976..252984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520235.4XP_011518537.1  26S proteasome non-ATPase regulatory subunit 13 isoform X1

    UniProtKB/TrEMBL
    J3KNQ3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    277982..293919
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369445.1XP_054225420.1  26S proteasome non-ATPase regulatory subunit 13 isoform X1