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CHMP3 charged multivesicular body protein 3 [ Homo sapiens (human) ]

Gene ID: 51652, updated on 7-Dec-2018

Summary

Official Symbol
CHMP3provided by HGNC
Official Full Name
charged multivesicular body protein 3provided by HGNC
Primary source
HGNC:HGNC:29865
See related
Ensembl:ENSG00000115561 MIM:610052
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NEDF; VPS24; CGI-149
Summary
This gene encodes a protein that sorts transmembrane proteins into lysosomes/vacuoles via the multivesicular body (MVB) pathway. This protein, along with other soluble coiled-coil containing proteins, forms part of the ESCRT-III protein complex that binds to the endosomal membrane and recruits additional cofactors for protein sorting into the MVB. This protein may also co-immunoprecipitate with a member of the IFG-binding protein superfamily. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream ring finger protein 103 (RNF103) gene. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in esophagus (RPKM 41.6), thyroid (RPKM 40.0) and 25 other tissues See more
Orthologs

Genomic context

See CHMP3 in Genome Data Viewer
Location:
2p11.2
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (86503430..86563497, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86730553..86790620, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene receptor accessory protein 1 Neighboring gene lysine demethylase 3A Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene uncharacterized LOC105374845 Neighboring gene ring finger protein 103 Neighboring gene required for meiotic nuclear division 5 homolog A

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Downregulation of guanine nucleotide-releasing protein, CD151/PETA-3, neuronatin, neuroendocrine differentiation factor, mitochondria 16s rRNA, and signal recognition particle is observed in HIV-1 infected and HIV-1 gp120-treated astrocytes PubMed
Pr55(Gag) gag Recruitment of CHMP2A and CHMP3 by CHMP4B to HIV-1 Gag puncta is observed in in-vitro membrane model PubMed
gag Replacing the NC-p1-p6 region of HIV-1 Gag with the leucine zipper domain of yeast GCN4 overcomes inhibition of HIV-1 particle budding by dominant-negative ESCRT proteins such as CHMP3 and Vps4A PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Budding and maturation of HIV virion, organism-specific biosystem (from REACTOME)
    Budding and maturation of HIV virion, organism-specific biosystemWith the virus components precariously assembled on the inner leaflet of the plasma membrane, the host cell machinery is required for viral budding. The virus takes advantage of the host ESCRT pathwa...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • ESCRT-III complex, organism-specific biosystem (from KEGG)
    ESCRT-III complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
  • ESCRT-III complex, conserved biosystem (from KEGG)
    ESCRT-III complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystem (from REACTOME)
    Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystemMany plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to th...
  • HIV Infection, organism-specific biosystem (from REACTOME)
    HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
  • HIV Life Cycle, organism-specific biosystem (from REACTOME)
    HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Internalization of ErbB1, organism-specific biosystem (from Pathway Interaction Database)
    Internalization of ErbB1, organism-specific biosystem
    Internalization of ErbB1
  • Late Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
    Late Phase of HIV Life Cycle, organism-specific biosystemThe late phase of the HIV-1 life cycle includes the regulated expression of the HIV gene products and the assembly of viral particles. The assembly of viral particles will be covered in a later relea...
  • Macroautophagy, organism-specific biosystem (from REACTOME)
    Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough RNF103-CHMP3

Readthrough gene: RNF103-CHMP3, Included gene: RNF103

Homology

Clone Names

  • FLJ38114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylcholine binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-specific protease binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
apoptotic process IEA
Inferred from Electronic Annotation
more info
 
autophagosome maturation TAS
Traceable Author Statement
more info
PubMed 
endosomal transport TAS
Traceable Author Statement
more info
 
endosome transport via multivesicular body sorting pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
late endosome to vacuole transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
macroautophagy TAS
Traceable Author Statement
more info
PubMed 
midbody abscission IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT mitotic metaphase plate congression IMP
Inferred from Mutant Phenotype
more info
PubMed 
multivesicular body assembly TAS
Traceable Author Statement
more info
PubMed 
multivesicular body sorting pathway TAS
Traceable Author Statement
more info
PubMed 
multivesicular body-lysosome fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of viral release from host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT nucleus organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of viral release from host cell IGI
Inferred from Genetic Interaction
more info
PubMed 
positive regulation of viral release from host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein heterooligomerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein polymerization IDA
Inferred from Direct Assay
more info
PubMed 
protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of centrosome duplication IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of early endosome to late endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of viral process IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral budding via host ESCRT complex IDA
Inferred from Direct Assay
more info
PubMed 
viral budding via host ESCRT complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral budding via host ESCRT complex TAS
Traceable Author Statement
more info
PubMed 
viral life cycle TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
ESCRT III complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ESCRT III complex IDA
Inferred from Direct Assay
more info
PubMed 
ESCRT III complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
multivesicular body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
charged multivesicular body protein 3
Names
25.1 protein
CHMP family, member 3
chromatin-modifying protein 3
neuroendocrine differentiation factor
vacuolar protein sorting 24 homolog
vacuolar protein sorting-associated protein 24

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001005753.2NP_001005753.1  charged multivesicular body protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001005753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. This results in translation initiation from a downstream start codon and an isoform (2, also known as Vps24beta) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC068288, AF151907, AK290725, DA290886
    Consensus CDS
    CCDS42707.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000386590.2, ENST00000409225.2
    Conserved Domains (1) summary
    cl21588
    Location:1121
    Snf7; Snf7
  2. NM_001193517.1NP_001180446.1  charged multivesicular body protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001180446.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AC068288, AF151907, AK129502, DA290886
    Consensus CDS
    CCDS54375.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000387045.1, ENST00000409727.5
    Conserved Domains (1) summary
    cl21588
    Location:18147
    Snf7; Snf7
  3. NM_016079.4NP_057163.1  charged multivesicular body protein 3 isoform 1

    See identical proteins and their annotated locations for NP_057163.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as Vps24alpha).
    Source sequence(s)
    AF151907, AK025046, AK312353, BC004419, BU192410, DA290886
    Consensus CDS
    CCDS33236.1
    UniProtKB/Swiss-Prot
    Q9Y3E7
    Related
    ENSP00000263856.4, ENST00000263856.8
    Conserved Domains (1) summary
    pfam03357
    Location:18187
    Snf7; Snf7

RNA

  1. NR_036454.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lack two internal exons in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region, as found in variant 1. Translation from the upstream start codon, as found in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC068288, AF151907, DA046087, DA290886

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    86503430..86563497 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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