Gene description for PSMD4
Gene name proteasome (prosome, macropain) 26S subunit, non-ATPase, 4
Gene symbol PSMD4
Other names/aliases AF
AF-1
ASF
MCB1
Rpn10
S5A
pUB-R5
Species Homo sapiens
 Database cross references - PSMD4
ExoCarta ExoCarta_5710
Entrez Gene 5710
HGNC 9561
MIM 601648
UniProt P55036  
 PSMD4 identified in exosomes derived from the following tissue/cell type
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Colorectal cancer cells 23161513    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Thymus 23844026    
 Gene ontology annotations for PSMD4
Molecular Function
    protein binding GO:0005515 IPI
    poly(A) RNA binding GO:0044822 IDA
    identical protein binding GO:0042802 IPI
Biological Process
    programmed cell death GO:0012501 TAS
    antigen processing and presentation of exogenous peptide antigen via MHC class I GO:0042590 TAS
    anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process GO:0031145 TAS
    apoptotic process GO:0006915 TAS
    stimulatory C-type lectin receptor signaling pathway GO:0002223 TAS
    regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle GO:0051439 TAS
    negative regulation of apoptotic process GO:0043066 TAS
    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent GO:0002479 TAS
    mitotic cell cycle GO:0000278 TAS
    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle GO:0051436 TAS
    negative regulation of canonical Wnt signaling pathway GO:0090090 TAS
    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest GO:0006977 TAS
    cellular nitrogen compound metabolic process GO:0034641 TAS
    positive regulation of canonical Wnt signaling pathway GO:0090263 TAS
    regulation of cellular amino acid metabolic process GO:0006521 TAS
    antigen processing and presentation of peptide antigen via MHC class I GO:0002474 TAS
    innate immune response GO:0045087 TAS
    viral process GO:0016032 TAS
    G1/S transition of mitotic cell cycle GO:0000082 TAS
    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition GO:0051437 TAS
    gene expression GO:0010467 TAS
    small molecule metabolic process GO:0044281 TAS
    protein polyubiquitination GO:0000209 TAS
    regulation of apoptotic process GO:0042981 TAS
Subcellular Localization
    nucleoplasm GO:0005654 TAS
    proteasome complex GO:0000502 IDA
    cytosol GO:0005829 TAS
    proteasome regulatory particle, base subcomplex GO:0008540 IEA
    proteasome accessory complex GO:0022624 ISS
    cytoplasm GO:0005737 IDA
 Experiment description of studies that identified PSMD4 in exosomes
1
Experiment ID 207
ISEV standards
EM
EV Biophysical techniques
TSG101|HSP70
EV Cytosolic markers
FLOT1
EV Membrane markers
VDAC
EV Negative markers
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DKO-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
2
Experiment ID 208
ISEV standards
EM
EV Biophysical techniques
TSG101|HSP70
EV Cytosolic markers
FLOT1
EV Membrane markers
VDAC
EV Negative markers
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name Dks-8
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
3
Experiment ID 209
ISEV standards
EV Biophysical techniques
TSG101|HSP70
EV Cytosolic markers
FLOT1
EV Membrane markers
VDAC
EV Negative markers
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23161513    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from mutant KRAS colon cancer cells identifies intercellular transfer of mutant KRAS.
Authors Demory Beckler M, Higginbotham JN, Franklin JL, Ham AJ, Halvey PJ, Imasuen IE, Whitwell C, Li M, Liebler DC, Coffey RJ.
Journal name Mol Cell Proteomics
Publication year 2012
Sample Colorectal cancer cells
Sample name DLD-1
Isolation/purification methods Differential centrifugation
Filtration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
Experiment ID 211
ISEV standards
EM
EV Biophysical techniques
TSG101|Alix
EV Cytosolic markers
EpCAM|TFRC
EV Membrane markers
cytochrome c|GOLGA2
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name IGROV1
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
5
Experiment ID 212
ISEV standards
CEM
EV Biophysical techniques
TSG101|Alix
EV Cytosolic markers
EpCAM|TFRC
EV Membrane markers
Cytochrome C|GOLGA2
EV Negative markers
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name OVCAR-3
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
6
Experiment ID 217
ISEV standards
EM
EV Biophysical techniques
TSG101
EV Cytosolic markers
CD81|CD9|CD63
EV Membrane markers
EV Negative markers
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O.
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for PSMD4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 PSMD13 5719
Affinity Capture-MS Homo sapiens
2 MYOD1  
Invivo Homo sapiens
Invitro Homo sapiens
Two-hybrid Homo sapiens
3 ID1  
Invivo Homo sapiens
Invitro Homo sapiens
Two-hybrid Homo sapiens
4 C12orf2  
Two-hybrid Homo sapiens
5 RAD23A  
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
6 NUB1 51667
Reconstituted Complex Homo sapiens
7 PSMD6 9861
Affinity Capture-MS Homo sapiens
8 PSMD10 5716
Affinity Capture-MS Homo sapiens
9 NEDD8 4738
Reconstituted Complex Homo sapiens
10 RAD23B 5887
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
11 TCF3  
Invitro Homo sapiens
View the network image/svg+xml
 Pathways in which PSMD4 is involved
PathwayEvidenceSource
Activation of NF-kappaB in B cells TAS Reactome
Antigen processing: Ubiquitination & Proteasome degradation TAS Reactome
APC/C:Cdc20 mediated degradation of Securin TAS Reactome
APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 TAS Reactome
Asymmetric localization of PCP proteins TAS Reactome
AUF1 (hnRNP D0) destabilizes mRNA TAS Reactome
Autodegradation of Cdh1 by Cdh1:APC/C TAS Reactome
Autodegradation of the E3 ubiquitin ligase COP1 TAS Reactome
Cdc20:Phospho-APC/C mediated degradation of Cyclin A TAS Reactome
CDK-mediated phosphorylation and removal of Cdc6 TAS Reactome
CDK-mediated phosphorylation and removal of Cdc6 TAS Reactome
CDT1 association with the CDC6:ORC:origin complex TAS Reactome
CLEC7A (Dectin-1) signaling TAS Reactome
Cross-presentation of soluble exogenous antigens (endosomes) TAS Reactome
Dectin-1 mediated noncanonical NF-kB signaling TAS Reactome
degradation of AXIN TAS Reactome
Degradation of beta-catenin by the destruction complex TAS Reactome
degradation of DVL TAS Reactome
Degradation of GLI1 by the proteasome TAS Reactome
Degradation of GLI2 by the proteasome TAS Reactome
ER-Phagosome pathway TAS Reactome
GLI3 is processed to GLI3R by the proteasome TAS Reactome
Hedgehog 'on' state TAS Reactome
Hedgehog ligand biogenesis TAS Reactome
Hh mutants that don't undergo autocatalytic processing are degraded by ERAD TAS Reactome
Orc1 removal from chromatin TAS Reactome
Orc1 removal from chromatin TAS Reactome
Regulation of activated PAK-2p34 by proteasome mediated degradation TAS Reactome
Regulation of ornithine decarboxylase (ODC) TAS Reactome
SCF(Skp2)-mediated degradation of p27/p21 TAS Reactome
SCF(Skp2)-mediated degradation of p27/p21 TAS Reactome
SCF-beta-TrCP mediated degradation of Emi1 TAS Reactome
Separation of Sister Chromatids TAS Reactome
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A TAS Reactome
Ubiquitin-dependent degradation of Cyclin D1 TAS Reactome
Vif-mediated degradation of APOBEC3G TAS Reactome
Vpu mediated degradation of CD4 TAS Reactome





Perform bioinformatics analysis of your extracellular vesicle data set using FunRich, a open access standalone tool. NEW UPDATED VERSION OF FunRich available for download (12/09/2016) from here