Gene description for VPS53
Gene name vacuolar protein sorting 53 homolog (S. cerevisiae)
Gene symbol VPS53
Other names/aliases HCCS1
PCH2E
hVps53L
pp13624
Species Homo sapiens
 Database cross references - VPS53
ExoCarta ExoCarta_55275
Vesiclepedia VP_55275
Entrez Gene 55275
HGNC 25608
MIM 615850
UniProt Q5VIR6  
 VPS53 identified in exosomes derived from the following tissue/cell type
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Chondrocytes 35931686    
Chondrocytes 35931686    
Thymus 23844026    
 Gene ontology annotations for VPS53
Molecular Function
    protein binding GO:0005515 IPI
Biological Process
    protein targeting to lysosome GO:0006622 IEA
    lysosomal transport GO:0007041 IMP
    endocytic recycling GO:0032456 IMP
    endocytic recycling GO:0032456 NAS
    retrograde transport, endosome to Golgi GO:0042147 IBA
    retrograde transport, endosome to Golgi GO:0042147 IMP
    retrograde transport, endosome to Golgi GO:0042147 NAS
    vesicle-mediated cholesterol transport GO:0090119 IEA
Subcellular Localization
    GARP complex GO:0000938 IBA
    GARP complex GO:0000938 IDA
    GARP complex GO:0000938 NAS
    Golgi apparatus GO:0005794 IDA
    cytosol GO:0005829 IDA
    endosome membrane GO:0010008 IEA
    membrane GO:0016020 IDA
    trans-Golgi network membrane GO:0032588 TAS
    intracellular membrane-bounded organelle GO:0043231 IDA
    perinuclear region of cytoplasm GO:0048471 IDA
    recycling endosome GO:0055037 IDA
    recycling endosome GO:0055037 NAS
    EARP complex GO:1990745 IDA
    EARP complex GO:1990745 IPI
 Experiment description of studies that identified VPS53 in exosomes
1
Experiment ID 489
MISEV standards
EM
Biophysical techniques
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
Canx
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 6
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
2
Experiment ID 490
MISEV standards
EM
Biophysical techniques
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
Canx
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
3
Experiment ID 491
MISEV standards
EM
Biophysical techniques
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
Canx
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 8
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
4
Experiment ID 492
MISEV standards
EM
Biophysical techniques
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
Canx
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors "Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ."
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 9
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
5
Experiment ID 497
MISEV standards
Biophysical techniques
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
6
Experiment ID 498
MISEV standards
EM
Biophysical techniques
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
7
Experiment ID 217
MISEV standards
EM
Biophysical techniques
TSG101|CD81|CD9|CD63
Enriched markers
Negative markers
NTA
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 VPS53
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 KRT37 8688
Affinity Capture-MS Homo sapiens
2 NUF2  
Affinity Capture-MS Homo sapiens
3 BLOC1S6  
Affinity Capture-MS Homo sapiens
4 RAB1A 5861
Synthetic Lethality Homo sapiens
5 LAMP3  
Proximity Label-MS Homo sapiens
6 ATG9A 79065
Proximity Label-MS Homo sapiens
7 CCDC132 55610
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 CEP170 9859
Affinity Capture-MS Homo sapiens
9 NUP62 23636
Affinity Capture-MS Homo sapiens
10 TRIM66  
Affinity Capture-MS Homo sapiens
11 THOC2 57187
Co-fractionation Homo sapiens
12 GRIPAP1 56850
Affinity Capture-MS Homo sapiens
13 LAMP2 3920
Proximity Label-MS Homo sapiens
14 TUFT1  
Affinity Capture-MS Homo sapiens
15 VPS54  
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
16 ARNTL  
Affinity Capture-MS Homo sapiens
17 SYCE3  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
18 EXOC1 55763
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
19 WHAMMP3  
Affinity Capture-MS Homo sapiens
20 PSMD9 5715
Affinity Capture-MS Homo sapiens
21 OIP5  
Affinity Capture-MS Homo sapiens
22 HAUS6  
Affinity Capture-MS Homo sapiens
23 STX6 10228
Affinity Capture-Western Homo sapiens
Proximity Label-MS Homo sapiens
24 POLR2C 5432
Proximity Label-MS Homo sapiens
25 VPS53 55275
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
26 PKN3 29941
Affinity Capture-MS Homo sapiens
27 USP7 7874
Co-fractionation Homo sapiens
28 THOC1 9984
Co-fractionation Homo sapiens
29 EBAG9 9166
Proximity Label-MS Homo sapiens
30 GPR17 2840
Affinity Capture-MS Homo sapiens
31 LAMTOR1 55004
Proximity Label-MS Homo sapiens
32 C15orf59  
Affinity Capture-MS Homo sapiens
33 RABGEF1 27342
Affinity Capture-MS Homo sapiens
34 KRT8 3856
Proximity Label-MS Homo sapiens
35 CLOCK  
Affinity Capture-MS Homo sapiens
36 S100A2 6273
Affinity Capture-MS Homo sapiens
37 VPS51 738
Reconstituted Complex Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
38 RABEP1 9135
Affinity Capture-MS Homo sapiens
39 RAB4A 5867
Proximity Label-MS Homo sapiens
40 DTNBP1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
41 KDM1A 23028
Affinity Capture-MS Homo sapiens
42 GIT2 9815
Affinity Capture-MS Homo sapiens
43 VCP 7415
Affinity Capture-MS Homo sapiens
44 GPR182  
Affinity Capture-MS Homo sapiens
45 EXOC6 54536
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
46 ENTHD1  
Affinity Capture-MS Homo sapiens
47 PTAR1 375743
Synthetic Lethality Homo sapiens
48 SNAP29 9342
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
49 YEATS4  
Affinity Capture-MS Homo sapiens
50 NCKAP5L  
Affinity Capture-MS Homo sapiens
51 GINS2  
Affinity Capture-MS Homo sapiens
52 EFNA4  
Affinity Capture-MS Homo sapiens
53 TSSC1 7260
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
54 CMKLR1 1240
Affinity Capture-MS Homo sapiens
55 PHLDB3  
Affinity Capture-MS Homo sapiens
56 RPRD1A  
Affinity Capture-MS Homo sapiens
57 TFPT  
Affinity Capture-MS Homo sapiens
58 PSMD7 5713
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
59 TXNDC9 10190
Co-fractionation Homo sapiens
60 RAB9A 9367
Proximity Label-MS Homo sapiens
61 PHF21A  
Affinity Capture-MS Homo sapiens
62 RABGAP1L 9910
Affinity Capture-MS Homo sapiens
63 HMG20A  
Affinity Capture-MS Homo sapiens
64 FLOT1 10211
Proximity Label-MS Homo sapiens
65 DZIP3  
Affinity Capture-MS Homo sapiens
66 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
67 TMEM9 252839
Affinity Capture-MS Homo sapiens
68 CEP170P1  
Affinity Capture-MS Homo sapiens
69 CCDC40  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
70 C10orf76  
Synthetic Lethality Homo sapiens
71 MAX  
Affinity Capture-MS Homo sapiens
72 CCHCR1  
Affinity Capture-MS Homo sapiens
73 VPS52 6293
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
74 VAMP4 8674
Affinity Capture-Western Homo sapiens
75 THAP11 57215
Affinity Capture-MS Homo sapiens
76 EXOC2 55770
Two-hybrid Homo sapiens
77 MKI67  
Affinity Capture-MS Homo sapiens
78 CCDC93 54520
Affinity Capture-MS Homo sapiens
79 TXNDC2  
Affinity Capture-MS Homo sapiens
80 BSG 682
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
81 RAB2A 5862
Proximity Label-MS Homo sapiens
82 KRT38 8687
Affinity Capture-MS Homo sapiens
83 GOLGA5 9950
Affinity Capture-MS Homo sapiens
84 RAB11A 8766
Proximity Label-MS Homo sapiens
85 ZUFSP 221302
Affinity Capture-MS Homo sapiens
86 KRAS 3845
Negative Genetic Homo sapiens
87 PRAF2 11230
Affinity Capture-MS Homo sapiens
88 PTRF 284119
Affinity Capture-MS Homo sapiens
89 RCOR1  
Affinity Capture-MS Homo sapiens
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