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Tchem
VPS4B
Vacuolar protein sorting-associated protein 4B

Protein Summary
Description
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). The protein encoded by this gene is a member of the AAA protein family (ATPases associated with di ...more
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000238497
  • ENSP00000238497
  • ENSG00000119541

Symbol
  • SKD1
  • VPS42
  • MIG1
  • SKD1
  • SKD1B
  • VPS4-2
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
kinase perturbation
0.99
molecular function
0.97
biological process
0.96
virus perturbation
0.94
histone modification site profile
0.9


Related Tools
Target Illumination GWAS Analytics (TIGA)
Thumbnail image for Target Illumination GWAS Analytics (TIGA)
TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
Thumbnail image for GENEVA
GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
Thumbnail image for GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 135.15   (req: < 5)
Gene RIFs: 24   (req: <= 3)
Antibodies: 169   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 135.15   (req: >= 5)
Gene RIFs: 24   (req: > 3)
Antibodies: 169   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 36
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 1
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Active Ligands (1)
1 – 1 of 1
CHEMBL4572843
Rendered image for CHEMBL4572843
GWAS Traits (6)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
creatinine measurement
1
1
1
35
monocyte percentage of leukocytes
1
1
1
33.1
glomerular filtration rate
1
1
1
33.1
eosinophil percentage of leukocytes
1
1
1
27.3
1
1
0
1.1
24.5
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
creatinine measurement
1
35
monocyte percentage of leukocytes
1
33.1
glomerular filtration rate
1
33.1
eosinophil percentage of leukocytes
1
27.3
0
1.1
24.5
Orthologs (15)
1 – 5 of 15
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
vacuolar protein sorting 4 homolog B
VGNC:5222
468565
Macaque
vacuolar protein sorting 4 homolog B
707614
Mouse
MGI:1100499
20479
Rat
RGD:1305969
360834
Dog
vacuolar protein sorting 4 homolog B
VGNC:48293
607306
Species
Name
OMA
EggNOG
Inparanoid
Chimp
vacuolar protein sorting 4 homolog B
Macaque
vacuolar protein sorting 4 homolog B
Mouse
Rat
Dog
vacuolar protein sorting 4 homolog B
Protein Structure (6 Structures, 1 AlphaFold Model)
RepresentationColor Scheme

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-O75351-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 6
PDB Structure Id
Ligand
Method
Resolution (Å)
Residues
Fraction of Total Protein
Pub Year
Title
PDB Structure Id
Fraction of Total Protein
Resolution
Pub Year
Pathways (12)
Budding and maturation of HIV virion (R-HSA-162588)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 5 of 9
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Budding and maturation of HIV virion
Reactome
Disease
Reactome
Endosomal Sorting Complex Required For Transport (ESCRT)
Reactome
HIV Infection
Reactome
HIV Life Cycle
Name
Explore in Pharos
Explore in Source
Budding and maturation of HIV virion
Disease
Endosomal Sorting Complex Required For Transport (ESCRT)
HIV Infection
HIV Life Cycle
Gene Ontology Terms (46)
Items per page:
10
1 – 6 of 6
GO Term
Evidence
Assigned by
Inferred from Direct Assay (IDA)
MGI
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Physical Interaction (IPI)
UniProtKB
Inferred from Electronic Annotation (IEA)
UniProtKB-KW
Protein-Protein Interactions (101)
1 – 10 of 101
VPS4A
Tbio
Novelty:  0.01508121
p_int:  0.999998837
p_ni:  0.000001163
Score:  0.986
Data Source:  BioPlex,Reactome,STRINGDB
ITPA
Tbio
Family:  Enzyme
Novelty:  0.00235169
p_int:  0.992453479
p_ni:  0.007545936
p_wrong:  5.85e-7
Score:  0.219
Data Source:  BioPlex,STRINGDB
EFR3A
Tbio
Novelty:  0.17687362
p_int:  0.978242895
p_ni:  0.020360284
p_wrong:  0.001396821
Score:  0.312
Data Source:  BioPlex,STRINGDB
RBM14
Tbio
Novelty:  0.01286049
p_int:  0.969669555
p_ni:  0.030301697
p_wrong:  0.000028748
Data Source:  BioPlex
BIRC2
Tchem
Novelty:  0.00199701
p_int:  0.869867978
p_ni:  0.130132011
p_wrong:  1.2e-8
Score:  0.228
Data Source:  BioPlex,STRINGDB
VTA1
Tbio
Novelty:  0.01697854
p_int:  0.839486604
p_ni:  0.160513396
Score:  0.999
Data Source:  BioPlex,Reactome,STRINGDB
RNF7
Tbio
Novelty:  0.02532658
p_int:  0.752510409
p_ni:  0.247489591
Data Source:  BioPlex
CHMP2B
Tbio
Novelty:  0.01116381
Score:  0.999
Data Source:  STRINGDB
CHMP2A
Tbio
Novelty:  0.00169253
Score:  0.999
Data Source:  STRINGDB
CHMP1A
Tbio
Novelty:  0.03969333
Score:  0.998
Data Source:  STRINGDB
Publication Statistics
PubMed Score  135.15

PubMed score by year
PubTator Score  35.56

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer
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