Gene description for Vps4b
Gene name vacuolar protein sorting 4b (yeast)
Gene symbol Vps4b
Other names/aliases 8030489C12Rik
Skd1
Species Mus musculus
 Database cross references - Vps4b
ExoCarta ExoCarta_20479
Vesiclepedia VP_20479
Entrez Gene 20479
UniProt P46467  
 Vps4b identified in exosomes derived from the following tissue/cell type
Colon cancer cells 37309723    
Macrophages 23658846    
Macrophages 23658846    
Macrophages 23658846    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Vps4b
Molecular Function
    DNA clamp loader activity GO:0003689 IEA
    protein binding GO:0005515 IPI
    ATP binding GO:0005524 IEA
    ATP hydrolysis activity GO:0016887 IBA
    ATP hydrolysis activity GO:0016887 ISO
    identical protein binding GO:0042802 ISO
    protein homodimerization activity GO:0042803 IEA
    protein homodimerization activity GO:0042803 ISO
    protein-containing complex binding GO:0044877 IEA
    protein-containing complex binding GO:0044877 ISO
    cohesin loader activity GO:0061775 IEA
    chromatin extrusion motor activity GO:0140584 IEA
    ATP-dependent H3-H4 histone complex chaperone activity GO:0140665 IEA
    ATP-dependent H2AZ histone chaperone activity GO:0140849 IEA
Biological Process
    angiogenesis GO:0001525 IMP
    plasma membrane repair GO:0001778 NAS
    chromatin remodeling GO:0006338 IEA
    potassium ion transport GO:0006813 IDA
    autophagy GO:0006914 NAS
    nucleus organization GO:0006997 ISO
    nucleus organization GO:0006997 NAS
    endosome organization GO:0007032 IGI
    endosome organization GO:0007032 IMP
    vacuole organization GO:0007033 IBA
    vacuolar transport GO:0007034 IMP
    mitotic metaphase chromosome alignment GO:0007080 IEA
    mitotic metaphase chromosome alignment GO:0007080 ISO
    central nervous system development GO:0007417 IMP
    regulation of centrosome duplication GO:0010824 ISO
    positive regulation of G2/M transition of mitotic cell cycle GO:0010971 IEA
    positive regulation of G2/M transition of mitotic cell cycle GO:0010971 ISO
    protein transport GO:0015031 IEA
    endosomal transport GO:0016197 IBA
    endosomal transport GO:0016197 ISO
    cholesterol transport GO:0030301 IMP
    nuclear membrane reassembly GO:0031468 NAS
    endosome to lysosome transport via multivesicular body sorting pathway GO:0032510 ISO
    response to lipid GO:0033993 IEA
    response to lipid GO:0033993 ISO
    multivesicular body assembly GO:0036258 IMP
    multivesicular body assembly GO:0036258 NAS
    viral budding via host ESCRT complex GO:0039702 IEA
    viral budding via host ESCRT complex GO:0039702 ISO
    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway GO:0043162 IEA
    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway GO:0043162 ISO
    viral budding from plasma membrane GO:0046761 IMP
    viral budding from plasma membrane GO:0046761 ISO
    protein depolymerization GO:0051261 IEA
    protein depolymerization GO:0051261 ISO
    canonical Wnt signaling pathway GO:0060070 IMP
    establishment of blood-brain barrier GO:0060856 IMP
    late endosomal microautophagy GO:0061738 IMP
    late endosome to lysosome transport via multivesicular body sorting pathway GO:0061764 NAS
    midbody abscission GO:0061952 ISO
    midbody abscission GO:0061952 NAS
    multivesicular body sorting pathway GO:0071985 NAS
    membrane fission GO:0090148 NAS
    ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway GO:0090611 IEA
    ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway GO:0090611 ISO
    autophagosome maturation GO:0097352 NAS
    chromatin looping GO:0140588 IEA
    regulation of mitotic spindle assembly GO:1901673 IEA
    regulation of mitotic spindle assembly GO:1901673 ISO
    negative regulation of exosomal secretion GO:1903542 IEA
    negative regulation of exosomal secretion GO:1903542 ISO
    positive regulation of exosomal secretion GO:1903543 IEA
    positive regulation of exosomal secretion GO:1903543 ISO
    positive regulation of centriole elongation GO:1903724 IEA
    positive regulation of centriole elongation GO:1903724 ISO
    ESCRT III complex disassembly GO:1904903 IEA
    ESCRT III complex disassembly GO:1904903 ISO
Subcellular Localization
    spindle pole GO:0000922 IEA
    spindle pole GO:0000922 ISO
    nucleus GO:0005634 ISO
    nuclear pore GO:0005643 NAS
    cytoplasm GO:0005737 ISO
    endosome GO:0005768 ISO
    centrosome GO:0005813 IEA
    centrosome GO:0005813 ISO
    cytosol GO:0005829 IDA
    plasma membrane GO:0005886 NAS
    endosome membrane GO:0010008 ISO
    midbody GO:0030496 NAS
    late endosome membrane GO:0031902 IEA
    Flemming body GO:0090543 IEA
    Flemming body GO:0090543 ISO
    ATPase complex GO:1904949 NAS
 Experiment description of studies that identified Vps4b in exosomes
1
Experiment ID 907
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample Colon cancer cells
Sample name C26
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
2
Experiment ID 214
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name Leishmania-infected-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
3
Experiment ID 215
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name LPS-treated-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
4
Experiment ID 216
MISEV standards
✔
EM
Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23658846    
Organism Mus musculus
Experiment description Immunomodulatory impact of leishmania-induced macrophage exosomes: a comparative proteomic and functional analysis.
Authors "Hassani K, Olivier M."
Journal name PLoS Negl Trop Dis
Publication year 2013
Sample Macrophages
Sample name Normal-Macrophage (J774A.1)
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Filtration
Protease inhibitors
Sucrose density gradient
Filtration
Ultracentrifugation
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
5
Experiment ID 908
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample T-cell lymphoma cells
Sample name EL4
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for Vps4b
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 SLC4A2 6522
Affinity Capture-MS Homo sapiens
2 CHMP2A 27243
Affinity Capture-MS Homo sapiens
3 ABCG2 9429
Affinity Capture-MS Homo sapiens
4 ATP6V0A1 535
Affinity Capture-MS Homo sapiens
5 ATP6V1B2 526
Affinity Capture-MS Homo sapiens
6 NOP14 8602
Affinity Capture-MS Homo sapiens
7 VPS9D1  
Affinity Capture-MS Homo sapiens
8 MUC13 56667
Affinity Capture-MS Homo sapiens
9 CHMP3 51652
Affinity Capture-MS Homo sapiens
10 CHMP1B 57132
Affinity Capture-MS Homo sapiens
11 TBC1D10A 83874
Affinity Capture-MS Homo sapiens
12 GPATCH4 54865
Affinity Capture-MS Homo sapiens
13 ATP6V0D1 9114
Affinity Capture-MS Homo sapiens
14 MITD1 129531
Affinity Capture-MS Homo sapiens
15 NSF 4905
Affinity Capture-MS Homo sapiens
16 GAR1 54433
Affinity Capture-MS Homo sapiens
17 PDCD6IP 10015
Affinity Capture-MS Homo sapiens
18 DDX19B 11269
Affinity Capture-MS Homo sapiens
19 ATP6V1G1 9550
Affinity Capture-MS Homo sapiens
20 ALB 213
Affinity Capture-MS Homo sapiens
21 Chmp4b 75608
Co-fractionation Mus musculus
22 CHMP1A 5119
Affinity Capture-MS Homo sapiens
23 Chmp1a  
Co-fractionation Mus musculus
24 BIN3 55909
Affinity Capture-MS Homo sapiens
25 C1orf52  
Affinity Capture-MS Homo sapiens
26 Chmp2a 68953
Affinity Capture-Western Mus musculus
Co-fractionation Mus musculus
27 CAPN7 23473
Affinity Capture-MS Homo sapiens
28 CALM1 801
Affinity Capture-MS Homo sapiens
29 VTA1 51534
Affinity Capture-MS Homo sapiens
30 GAS2L3  
Affinity Capture-MS Homo sapiens
31 IMPACT 55364
Affinity Capture-MS Homo sapiens
32 ATP11C 286410
Affinity Capture-MS Homo sapiens
33 TMEM55B 90809
Affinity Capture-MS Homo sapiens
34 SCNM1  
Affinity Capture-MS Homo sapiens
35 ATP6V1F 9296
Affinity Capture-MS Homo sapiens
36 UVRAG  
Affinity Capture-MS Homo sapiens
37 Tmem173  
Proximity Label-MS Mus musculus
38 MED21  
Affinity Capture-MS Homo sapiens
39 Vta1 66201
Affinity Capture-Western Mus musculus
Co-fractionation Mus musculus
Co-fractionation Mus musculus
40 CHMP4B 128866
Affinity Capture-MS Homo sapiens
41 CNOT1 23019
Affinity Capture-MS Homo sapiens
42 Ist1 71955
Co-fractionation Mus musculus
43 IST1 9798
Affinity Capture-MS Homo sapiens
44 SARAF  
Affinity Capture-MS Homo sapiens
45 ATP6V1A 523
Affinity Capture-MS Homo sapiens
46 CSNK2A2 1459
Affinity Capture-MS Homo sapiens
47 ARHGAP11A  
Affinity Capture-MS Homo sapiens
48 CHMP5 51510
Affinity Capture-MS Homo sapiens
49 RPRD1B 58490
Affinity Capture-MS Homo sapiens
50 SPAST 6683
Affinity Capture-MS Homo sapiens
51 ZER1 10444
Affinity Capture-MS Homo sapiens
52 TIMM23 100287932
Affinity Capture-MS Homo sapiens
53 BRAF  
Affinity Capture-MS Homo sapiens
54 CCDC88A 55704
Affinity Capture-MS Homo sapiens
55 Chmp5 76959
Co-fractionation Mus musculus
56 STX18 53407
Affinity Capture-MS Homo sapiens
57 CHMP2B 25978
Affinity Capture-MS Homo sapiens
58 FLOT2 2319
Affinity Capture-MS Homo sapiens
59 DNAJC13 23317
Affinity Capture-MS Homo sapiens
60 RAD51  
Affinity Capture-MS Homo sapiens
61 FLOT1 10211
Affinity Capture-MS Homo sapiens
62 CDT1  
Affinity Capture-MS Homo sapiens
63 DERL1 79139
Affinity Capture-MS Homo sapiens
64 GPRC5A 9052
Affinity Capture-MS Homo sapiens
65 CHMP4A 29082
Affinity Capture-MS Homo sapiens
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