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Q9HD42 (CHM1A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Charged multivesicular body protein 1a
Alternative name(s):
Chromatin-modifying protein 1a
Short name=CHMP1a
Vacuolar protein sorting-associated protein 46-1
Short name=Vps46-1
Short name=hVps46-1
Gene names
Name:CHMP1A
Synonyms:CHMP1, KIAA0047, PCOLN3, PRSM1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length196 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. 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. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B to the midbody of dividing cells. May also be involved in chromosome condensation. Targets the Polycomb group (PcG) protein BMI1/PCGF4 to regions of condensed chromatin. May play a role in stable cell cycle progression and in PcG gene silencing. Ref.1 Ref.2 Ref.7 Ref.13 Ref.17

Subunit structure

Probable peripherally associated component of the endosomal sorting required for transport complex III (ESCRT-III). ESCRT-III components are thought to multimerize to form a flat lattice on the perimeter membrane of the endosome. Several assembly forms of ESCRT-III may exist that interact and act sequentally. Self-associates. Interacts with CHMP1B. Interacts with VPS4A. Interacts with VPS4B. Interacts with PHF1. Interacts with IST1. Interacts with MITD1. Ref.7 Ref.8 Ref.9 Ref.12 Ref.13 Ref.17

Subcellular location

Cytoplasm. Endosome membrane; Peripheral membrane protein. Nucleus matrix. Note: The cytoplasmic form is partially membrane-associated and localizes to early endosomes. The nuclear form remains associated with the chromosome scaffold during mitosis. On overexpression, it localizes to nuclear bodies characterized by nuclease-resistant condensed chromatin. Ref.2 Ref.7

Tissue specificity

Expressed in placenta, cultured skin fibroblasts and in osteoblast cell line MG-63. Ref.1

Induction

By muristerone. Ref.2

Involvement in disease

Pontocerebellar hypoplasia 8 (PCH8) [MIM:614961]: An autosomal recessive neurodevelopmental disorder characterized by severe psychomotor retardation, abnormal movements, hypotonia, spasticity, and variable visual defects. Brain MRI shows pontocerebellar hypoplasia, decreased cerebral white matter, and a thin corpus callosum.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.15

Sequence similarities

Belongs to the SNF7 family.

Caution

Was originally (Ref.1) thought to be a metalloprotease (PRSM1). This was based on a wrong translation of the ORF which gave rise to a putative protein of 318 AA containing a pattern reminiscent of zinc metalloproteases.

Sequence caution

The sequence AAC50775.1 differs from that shown. Reason: Erroneous translation. Wrong choice of frame.

The sequence BAA07557.1 differs from that shown. Reason: Erroneous translation. Wrong choice of frame.

Ontologies

Keywords
   Biological processCell cycle
Cell division
Protein transport
Transcription
Transcription regulation
Transport
   Cellular componentCytoplasm
Endosome
Membrane
Nucleus
   Coding sequence diversityAlternative splicing
   DomainCoiled coil
   Molecular functionRepressor
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcytokinesis

Inferred from mutant phenotype Ref.13. Source: UniProtKB

gene silencing

Inferred from direct assay Ref.2. Source: UniProtKB

mitotic chromosome condensation

Inferred from direct assay Ref.2. Source: UniProtKB

negative regulation of transcription by glucose

Inferred from direct assay PubMed 9837962. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from direct assay Ref.2. Source: UniProtKB

protein transport

Inferred from electronic annotation. Source: UniProtKB-KW

proteolysis

Traceable author statement Ref.1. Source: GOC

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

vesicle-mediated transport

Inferred from direct assay Ref.7. Source: UniProtKB

   Cellular_componentcondensed nuclear chromosome

Inferred from direct assay Ref.2. Source: UniProtKB

early endosome

Inferred from direct assay Ref.7. Source: UniProtKB

endomembrane system

Inferred from direct assay Ref.7. Source: UniProtKB

endosome membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

extracellular vesicular exosome

Inferred from direct assay PubMed 19056867PubMed 23376485. Source: UniProt

microtubule organizing center

Inferred from direct assay Ref.7. Source: UniProtKB

nuclear matrix

Inferred from direct assay Ref.2. Source: UniProtKB

   Molecular_functionmetallopeptidase activity

Traceable author statement Ref.1. Source: ProtInc

protein binding

Inferred from physical interaction Ref.7PubMed 12445808Ref.13Ref.12. Source: UniProtKB

protein domain specific binding

Inferred from physical interaction Ref.16. Source: UniProtKB

zinc ion binding

Traceable author statement Ref.1. Source: ProtInc

Complete GO annotation...

Binary interactions

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 Ref.2 (identifier: Q9HD42-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9HD42-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-128: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 196196Charged multivesicular body protein 1a
PRO_0000211448

Regions

Coiled coil5 – 4743 Potential
Coiled coil102 – 12423 Potential
Motif185 – 19511MIT-interacting motif

Amino acid modifications

Modified residue11N-acetylmethionine Ref.11

Natural variations

Alternative sequence1 – 128128Missing in isoform 2.
VSP_051716

Experimental info

Mutagenesis1911L → A: No effect on interaction with IST1; when associated with L-194. Ref.13
Mutagenesis1941L → A: No effect on interaction with IST1; when associated with L-194. Ref.13
Sequence conflict771Q → D in AAC50775. Ref.1

Secondary structure

... 196
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 85D0ED7D10828D60

FASTA19621,703
        10         20         30         40         50         60 
MDDTLFQLKF TAKQLEKLAK KAEKDSKAEQ AKVKKALLQK NVECARVYAE NAIRKKNEGV 

        70         80         90        100        110        120 
NWLRMASRVD AVASKVQTAV TMKGVTKNMA QVTKALDKAL STMDLQKVSS VMDRFEQQVQ 

       130        140        150        160        170        180 
NLDVHTSVME DSMSSATTLT TPQEQVDSLI MQIAEENGLE VLDQLSQLPE GASAVGESSV 

       190 
RSQEDQLSRR LAALRN 

« Hide

Isoform 2 [UniParc].

Checksum: F58834B1C0E254DB
Show »

FASTA687,363

References

« Hide 'large scale' references
[1]"Molecular cloning, expression and chromosomal localization of a human gene encoding a 33 kDa putative metallopeptidase (PRSM1)."
Scott I.C., Halila R., Jenkins J.M., Mehan S., Apostolou S., Winqvist R., Callen D.F., Prockop D.J., Peltonen L., Kadler K.E.
Gene 174:135-143(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], PRELIMINARY FUNCTION, TISSUE SPECIFICITY.
Tissue: Fibroblast and Placenta.
[2]"CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression."
Stauffer D.R., Howard T.L., Nyun T., Hollenberg S.M.
J. Cell Sci. 114:2383-2393(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, INDUCTION.
Tissue: Placenta.
[3]"Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1."
Nomura N., Nagase T., Miyajima N., Sazuka T., Tanaka A., Sato S., Seki N., Kawarabayasi Y., Ishikawa K., Tabata S.
DNA Res. 1:223-229(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Bone marrow.
[4]"Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[5]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Tissue: Brain and Kidney.
[7]"CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins."
Howard T.L., Stauffer D.R., Degnin C.R., Hollenberg S.M.
J. Cell Sci. 114:2395-2404(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH VPS4A.
[8]"The protein network of HIV budding."
von Schwedler U.K., Stuchell M., Mueller B., Ward D.M., Chung H.-Y., Morita E., Wang H.E., Davis T., He G.P., Cimbora D.M., Scott A., Kraeusslich H.-G., Kaplan J., Morham S.G., Sundquist W.I.
Cell 114:701-713(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CHMP1B; VPS4A AND VPS4B.
[9]"Divergent retroviral late-budding domains recruit vacuolar protein sorting factors by using alternative adaptor proteins."
Martin-Serrano J., Yarovoy A., Perez-Caballero D., Bieniasz P.D.
Proc. Natl. Acad. Sci. U.S.A. 100:12414-12419(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SELF-ASSOCIATION, INTERACTION WITH CHMP1B AND VPS4A.
[10]Erratum
Martin-Serrano J., Yarovoy A., Perez-Caballero D., Bieniasz P.D.
Proc. Natl. Acad. Sci. U.S.A. 100:152845-152845(2003)
[11]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Essential role of hIST1 in cytokinesis."
Agromayor M., Carlton J.G., Phelan J.P., Matthews D.R., Carlin L.M., Ameer-Beg S., Bowers K., Martin-Serrano J.
Mol. Biol. Cell 20:1374-1387(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH IST1.
[13]"Biochemical analyses of human IST1 and its function in cytokinesis."
Bajorek M., Morita E., Skalicky J.J., Morham S.G., Babst M., Sundquist W.I.
Mol. Biol. Cell 20:1360-1373(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH IST1, MUTAGENESIS OF LEU-191 AND LEU-194.
[14]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development."
Mochida G.H., Ganesh V.S., de Michelena M.I., Dias H., Atabay K.D., Kathrein K.L., Huang H.T., Hill R.S., Felie J.M., Rakiec D., Gleason D., Hill A.D., Malik A.N., Barry B.J., Partlow J.N., Tan W.H., Glader L.J., Barkovich A.J. expand/collapse author list , Dobyns W.B., Zon L.I., Walsh C.A.
Nat. Genet. 44:1260-1264(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN PCH8.
[16]"ESCRT-III recognition by VPS4 ATPases."
Stuchell-Brereton M.D., Skalicky J.J., Kieffer C., Karren M.A., Ghaffarian S., Sundquist W.I.
Nature 449:740-744(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 180-196 IN COMPLEX WITH VPS4A.
[17]"ESCRT-III binding protein MITD1 is involved in cytokinesis and has an unanticipated PLD fold that binds membranes."
Hadders M.A., Agromayor M., Obita T., Perisic O., Caballe A., Kloc M., Lamers M.H., Williams R.L., Martin-Serrano J.
Proc. Natl. Acad. Sci. U.S.A. 109:17424-17429(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) OF 184-196 IN COMPLEX WITH MITD1, FUNCTION, INTERACTION WITH MITD1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U58048 mRNA. Translation: AAC50775.1. Sequence problems.
AF281063 mRNA. Translation: AAG01448.1.
D38554 mRNA. Translation: BAA07557.1. Sequence problems.
BT006841 mRNA. Translation: AAP35487.1.
AC010538 Genomic DNA. No translation available.
BC007527 mRNA. No translation available.
BC010000 mRNA. Translation: AAH10000.2.
BC132711 mRNA. Translation: AAI32712.1.
BC132713 mRNA. Translation: AAI32714.1.
CCDSCCDS45552.1. [Q9HD42-1]
PIRJC4963.
RefSeqNP_002759.2. NM_002768.4. [Q9HD42-1]
UniGeneHs.589427.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2JQ9NMR-B180-196[»]
2YMBX-ray3.40F/H184-196[»]
4A5XX-ray1.91C/D184-196[»]
ProteinModelPortalQ9HD42.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111148. 14 interactions.
DIPDIP-50647N.
IntActQ9HD42. 5 interactions.
MINTMINT-6946738.
STRING9606.ENSP00000253475.

PTM databases

PhosphoSiteQ9HD42.

Polymorphism databases

DMDM62510514.

Proteomic databases

MaxQBQ9HD42.
PaxDbQ9HD42.
PRIDEQ9HD42.

Protocols and materials databases

DNASU5119.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000397901; ENSP00000380998; ENSG00000131165. [Q9HD42-1]
GeneID5119.
KEGGhsa:5119.
UCSCuc002fnu.4. human. [Q9HD42-1]

Organism-specific databases

CTD5119.
GeneCardsGC16M089710.
H-InvDBHIX0013363.
HGNCHGNC:8740. CHMP1A.
MIM164010. gene.
614961. phenotype.
neXtProtNX_Q9HD42.
Orphanet324569. Pontocerebellar hypoplasia type 8.
PharmGKBPA33085.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG331649.
HOGENOMHOG000241980.
HOVERGENHBG080200.
OrthoDBEOG7BP843.
PhylomeDBQ9HD42.
TreeFamTF300076.

Gene expression databases

ArrayExpressQ9HD42.
BgeeQ9HD42.
CleanExHS_CHMP1A.
GenevestigatorQ9HD42.

Family and domain databases

InterProIPR005024. Snf7.
[Graphical view]
PfamPF03357. Snf7. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCHMP1A. human.
EvolutionaryTraceQ9HD42.
GeneWikiCHMP1A.
GenomeRNAi5119.
NextBio19738.
PROQ9HD42.
SOURCESearch...

Entry information

Entry nameCHM1A_HUMAN
AccessionPrimary (citable) accession number: Q9HD42
Secondary accession number(s): A2RU09 expand/collapse secondary AC list , Q14468, Q15779, Q96G31
Entry history
Integrated into UniProtKB/Swiss-Prot: April 12, 2005
Last sequence update: March 1, 2001
Last modified: July 9, 2014
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM