Browse VPS4B

Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Prevacuolar compartment membrane; Peripheral membrane protein. Late endosome membrane Peripheral membrane protein Note=Membrane-associated in the prevacuolar endosomal compartment. Localized in HIV-1 particles purified from acutely infected cells.
Domain PF00004 ATPase family associated with various cellular activities (AAA)
PF04212 MIT (microtubule interacting and transport) domain
PF09336 Vps4 C terminal oligomerisation domain
Function

Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses). VPS4A/B are required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413).

> Gene Ontology
 
Biological Process GO:0000070 mitotic sister chromatid segregation
GO:0000086 G2/M transition of mitotic cell cycle
GO:0000226 microtubule cytoskeleton organization
GO:0000819 sister chromatid segregation
GO:0000920 cell separation after cytokinesis
GO:0006813 potassium ion transport
GO:0006869 lipid transport
GO:0006887 exocytosis
GO:0006900 membrane budding
GO:0006914 autophagy
GO:0006997 nucleus organization
GO:0007032 endosome organization
GO:0007033 vacuole organization
GO:0007034 vacuolar transport
GO:0007041 lysosomal transport
GO:0007051 spindle organization
GO:0007059 chromosome segregation
GO:0007067 mitotic nuclear division
GO:0007080 mitotic metaphase plate congression
GO:0007088 regulation of mitotic nuclear division
GO:0007098 centrosome cycle
GO:0007099 centriole replication
GO:0007346 regulation of mitotic cell cycle
GO:0008333 endosome to lysosome transport
GO:0010389 regulation of G2/M transition of mitotic cell cycle
GO:0010824 regulation of centrosome duplication
GO:0010825 positive regulation of centrosome duplication
GO:0010876 lipid localization
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
GO:0015672 monovalent inorganic cation transport
GO:0015850 organic hydroxy compound transport
GO:0015918 sterol transport
GO:0016050 vesicle organization
GO:0016197 endosomal transport
GO:0017157 regulation of exocytosis
GO:0019058 viral life cycle
GO:0019068 virion assembly
GO:0019076 viral release from host cell
GO:0030301 cholesterol transport
GO:0031023 microtubule organizing center organization
GO:0032509 endosome transport via multivesicular body sorting pathway
GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway
GO:0032886 regulation of microtubule-based process
GO:0032984 macromolecular complex disassembly
GO:0036257 multivesicular body organization
GO:0036258 multivesicular body assembly
GO:0039702 viral budding via host ESCRT complex
GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0043241 protein complex disassembly
GO:0043624 cellular protein complex disassembly
GO:0043900 regulation of multi-organism process
GO:0043902 positive regulation of multi-organism process
GO:0043903 regulation of symbiosis, encompassing mutualism through parasitism
GO:0044089 positive regulation of cellular component biogenesis
GO:0044770 cell cycle phase transition
GO:0044772 mitotic cell cycle phase transition
GO:0044803 multi-organism membrane organization
GO:0044839 cell cycle G2/M phase transition
GO:0045787 positive regulation of cell cycle
GO:0045920 negative regulation of exocytosis
GO:0045921 positive regulation of exocytosis
GO:0045931 positive regulation of mitotic cell cycle
GO:0046599 regulation of centriole replication
GO:0046601 positive regulation of centriole replication
GO:0046605 regulation of centrosome cycle
GO:0046607 positive regulation of centrosome cycle
GO:0046755 viral budding
GO:0048524 positive regulation of viral process
GO:0050000 chromosome localization
GO:0050792 regulation of viral process
GO:0051047 positive regulation of secretion
GO:0051048 negative regulation of secretion
GO:0051051 negative regulation of transport
GO:0051225 spindle assembly
GO:0051261 protein depolymerization
GO:0051297 centrosome organization
GO:0051298 centrosome duplication
GO:0051303 establishment of chromosome localization
GO:0051310 metaphase plate congression
GO:0051493 regulation of cytoskeleton organization
GO:0051495 positive regulation of cytoskeleton organization
GO:0051640 organelle localization
GO:0051656 establishment of organelle localization
GO:0051783 regulation of nuclear division
GO:0060627 regulation of vesicle-mediated transport
GO:0061511 centriole elongation
GO:0061738 late endosomal microautophagy
GO:0070507 regulation of microtubule cytoskeleton organization
GO:0090068 positive regulation of cell cycle process
GO:0090169 regulation of spindle assembly
GO:0090224 regulation of spindle organization
GO:0090307 mitotic spindle assembly
GO:0090611 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway
GO:0098534 centriole assembly
GO:0098813 nuclear chromosome segregation
GO:1901673 regulation of mitotic spindle assembly
GO:1901987 regulation of cell cycle phase transition
GO:1901989 positive regulation of cell cycle phase transition
GO:1901990 regulation of mitotic cell cycle phase transition
GO:1901992 positive regulation of mitotic cell cycle phase transition
GO:1902115 regulation of organelle assembly
GO:1902117 positive regulation of organelle assembly
GO:1902186 regulation of viral release from host cell
GO:1902188 positive regulation of viral release from host cell
GO:1902590 multi-organism organelle organization
GO:1902592 multi-organism membrane budding
GO:1902749 regulation of cell cycle G2/M phase transition
GO:1902751 positive regulation of cell cycle G2/M phase transition
GO:1902850 microtubule cytoskeleton organization involved in mitosis
GO:1903531 negative regulation of secretion by cell
GO:1903532 positive regulation of secretion by cell
GO:1903541 regulation of exosomal secretion
GO:1903542 negative regulation of exosomal secretion
GO:1903543 positive regulation of exosomal secretion
GO:1903722 regulation of centriole elongation
GO:1903724 positive regulation of centriole elongation
GO:1903900 regulation of viral life cycle
GO:1903902 positive regulation of viral life cycle
GO:1904896 ESCRT complex disassembly
GO:1904903 ESCRT III complex disassembly
GO:1990182 exosomal secretion
Molecular Function GO:0008022 protein C-terminus binding
GO:0016887 ATPase activity
GO:0042623 ATPase activity, coupled
Cellular Component GO:0000922 spindle pole
GO:0005770 late endosome
GO:0005813 centrosome
GO:0005819 spindle
GO:0010008 endosome membrane
GO:0030496 midbody
GO:0031902 late endosome membrane
GO:0044440 endosomal part
GO:0090543 Flemming body
> KEGG and Reactome Pathway
 
KEGG hsa04144 Endocytosis
Reactome R-HSA-162588: Budding and maturation of HIV virion
R-HSA-1643685: Disease
R-HSA-917729: Endosomal Sorting Complex Required For Transport (ESCRT)
R-HSA-162906: HIV Infection
R-HSA-162587: HIV Life Cycle
R-HSA-5663205: Infectious disease
R-HSA-162599: Late Phase of HIV Life Cycle
R-HSA-199991: Membrane Trafficking
R-HSA-5653656: Vesicle-mediated transport
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between VPS4B and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of VPS4B in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell logFC: -2.68; FDR: 0.04630 Resistant to T cell-mediated killing
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell logFC: -2.97; FDR: 0.01650 Resistant to T cell-mediated killing
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NS NA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NS NA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NS NA/NS
24476824shRNAmelanomaB16Primary screen NA/NS NA/NS
24476824shRNAmelanomaB16Secondary screen NA/NS NA/NS
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of VPS4B in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)14120.1050.699
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.1510.941
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)870.0730.96
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.3760.353
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590.3230.859
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.4460.848
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.2170.572
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.3350.843
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.0450.982
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.3120.808
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.6890.729
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.1580.00408
> Mutation difference between responders and non-responders
 

There is no record.
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of VPS4B. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of VPS4B. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by VPS4B.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of VPS4B. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of VPS4B expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between VPS4B and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolVPS4B
Namevacuolar protein sorting 4 homolog B (S. cerevisiae)
Aliases VPS4-2; SKD1B; suppressor of K+ transport defect 1; vacuolar protein sorting 4B (yeast); MIG1; cell migratio ......
Chromosomal Location18q21.33
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting VPS4B collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.