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Protein

Vacuolar protein sorting-associated protein 11 homolog

Gene

VPS11

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203). Involved in cargo transport from early to late endosomes and required for the transition from early to late endosomes (PubMed:21148287). Involved in the retrograde Shiga toxin transport (PubMed:23593995).5 Publications3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri822 – 861RING-typePROSITE-ProRule annotationAdd BLAST40

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • nucleotide binding Source: UniProtKB-KW
  • protein binding, bridging Source: GO_Central
  • protein domain specific binding Source: UniProtKB
  • syntaxin binding Source: UniProtKB

GO - Biological processi

  • autophagy Source: UniProtKB-KW
  • endosomal vesicle fusion Source: UniProtKB
  • endosome organization Source: GO_Central
  • endosome to lysosome transport Source: UniProtKB
  • intracellular protein transport Source: InterPro
  • lysosome organization Source: GO_Central
  • positive regulation of cellular protein catabolic process Source: UniProtKB
  • positive regulation of early endosome to late endosome transport Source: UniProtKB
  • positive regulation of protein targeting to mitochondrion Source: ParkinsonsUK-UCL
  • regulation of organelle assembly Source: UniProtKB
  • regulation of protein stability Source: ParkinsonsUK-UCL
  • regulation of SNARE complex assembly Source: GO_Central
  • vesicle docking involved in exocytosis Source: GO_Central

Keywordsi

Biological processAutophagy, Protein transport, Transport
LigandMetal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Vacuolar protein sorting-associated protein 11 homolog
Short name:
hVPS11
Alternative name(s):
RING finger protein 108
Gene namesi
Name:VPS11
Synonyms:RNF108
ORF Names:PP3476
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000160695.14.
HGNCiHGNC:14583. VPS11.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasmic vesicle, Endosome, Lysosome, Membrane

Pathology & Biotechi

Involvement in diseasei

Leukodystrophy, hypomyelinating, 12 (HLD12)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive neurologic disorder characterized by developmental delay, spasticity, truncal hypotonia, acquired microcephaly, intellectual disability with variable seizure disorder, accompanied by thin corpus callosum, paucity of white matter and delayed myelination.
See also OMIM:616683
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_076393846C → G in HLD12. 1 Publication1

Keywords - Diseasei

Disease mutation, Leukodystrophy

Organism-specific databases

DisGeNETi55823.
MalaCardsiVPS11.
MIMi616683. phenotype.
PharmGKBiPA37902.

Polymorphism and mutation databases

BioMutaiVPS11.
DMDMi23396928.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000559022 – 941Vacuolar protein sorting-associated protein 11 homologAdd BLAST940

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei813PhosphoserineCombined sources1
Modified residuei904Omega-N-methylarginineBy similarity1
Modified residuei924PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiQ9H270.
MaxQBiQ9H270.
PeptideAtlasiQ9H270.
PRIDEiQ9H270.

PTM databases

iPTMnetiQ9H270.
PhosphoSitePlusiQ9H270.

Expressioni

Tissue specificityi

Ubiquitous. Expression was highest in heart and low in lung.

Gene expression databases

BgeeiENSG00000160695.
CleanExiHS_VPS11.
ExpressionAtlasiQ9H270. baseline and differential.
GenevisibleiQ9H270. HS.

Organism-specific databases

HPAiHPA039020.

Interactioni

Subunit structurei

Core component of at least two putative endosomal tethering complexes, the homotypic fusion and vacuole protein sorting (HOPS) complex and the class C core vacuole/endosome tethering (CORVET) complex. Their common core is composed of the class C Vps proteins VPS11, VPS16, VPS18 and VPS33A, which in HOPS further associates with VPS39 and VPS41 and in CORVET with VPS8 and TGFBRAP1 (PubMed:11382755, PubMed:20434987, PubMed:23351085, PubMed:23901104, PubMed:25266290, PubMed:25783203). Interacts with TGFBRAP1, MON1B, STX7, STX17, EZR, RDX, MSN, ECM29 (PubMed:11382755, PubMed:20682791, PubMed:21148287, PubMed:24554770, PubMed:25266290). Interacts with RAB5C (By similarity). Associates with adaptor protein complex 3 (AP-3) and clathrin:AP-3 complexes (By similarity).By similarity3 Publications7 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • protein binding, bridging Source: GO_Central
  • protein domain specific binding Source: UniProtKB
  • syntaxin binding Source: UniProtKB

Protein-protein interaction databases

BioGridi120930. 56 interactors.
CORUMiQ9H270.
IntActiQ9H270. 35 interactors.
MINTiMINT-1402371.

Structurei

3D structure databases

ProteinModelPortaliQ9H270.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati411 – 561CHCR 1Add BLAST151
Repeati572 – 736CHCR 2Add BLAST165

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili772 – 813Sequence analysisAdd BLAST42

Sequence similaritiesi

Belongs to the VPS11 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri822 – 861RING-typePROSITE-ProRule annotationAdd BLAST40

Keywords - Domaini

Coiled coil, Repeat, Zinc-finger

Phylogenomic databases

HOGENOMiHOG000216424.
HOVERGENiHBG055822.
InParanoidiQ9H270.
KOiK20179.
PhylomeDBiQ9H270.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR016024. ARM-type_fold.
IPR000547. Clathrin_H-chain/VPS_repeat.
IPR011990. TPR-like_helical_dom_sf.
IPR016528. VPS11.
IPR024763. VPS11_C.
IPR015943. WD40/YVTN_repeat-like_dom_sf.
IPR036322. WD40_repeat_dom_sf.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
PANTHERiPTHR23323:SF24. PTHR23323:SF24. 1 hit.
PfamiView protein in Pfam
PF00637. Clathrin. 1 hit.
PF12451. VPS11_C. 1 hit.
PIRSFiPIRSF007860. VPS11. 1 hit.
SMARTiView protein in SMART
SM00184. RING. 1 hit.
SUPFAMiSSF48371. SSF48371. 1 hit.
SSF50978. SSF50978. 1 hit.
PROSITEiView protein in PROSITE
PS50236. CHCR. 2 hits.
PS50089. ZF_RING_2. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9H270-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAYLQWRRF VFFDKELVKE PLSNDGAAPG ATPASGSAAS KFLCLPPGIT
60 70 80 90 100
VCDSGRGSLV FGDMEGQIWF LPRSLQLTGF QAYKLRVTHL YQLKQHNILA
110 120 130 140 150
SVGEDEEGIN PLVKIWNLEK RDGGNPLCTR IFPAIPGTEP TVVSCLTVHE
160 170 180 190 200
NLNFMAIGFT DGSVTLNKGD ITRDRHSKTQ ILHKGNYPVT GLAFRQAGKT
210 220 230 240 250
THLFVVTTEN VQSYIVSGKD YPRVELDTHG CGLRCSALSD PSQDLQFIVA
260 270 280 290 300
GDECVYLYQP DERGPCFAFE GHKLIAHWFR GYLIIVSRDR KVSPKSEFTS
310 320 330 340 350
RDSQSSDKQI LNIYDLCNKF IAYSTVFEDV VDVLAEWGSL YVLTRDGRVH
360 370 380 390 400
ALQEKDTQTK LEMLFKKNLF EMAINLAKSQ HLDSDGLAQI FMQYGDHLYS
410 420 430 440 450
KGNHDGAVQQ YIRTIGKLEP SYVIRKFLDA QRIHNLTAYL QTLHRQSLAN
460 470 480 490 500
ADHTTLLLNC YTKLKDSSKL EEFIKKKSES EVHFDVETAI KVLRQAGYYS
510 520 530 540 550
HALYLAENHA HHEWYLKIQL EDIKNYQEAL RYIGKLPFEQ AESNMKRYGK
560 570 580 590 600
ILMHHIPEQT TQLLKGLCTD YRPSLEGRSD REAPGCRANS EEFIPIFANN
610 620 630 640 650
PRELKAFLEH MSEVQPDSPQ GIYDTLLELR LQNWAHEKDP QVKEKLHAEA
660 670 680 690 700
ISLLKSGRFC DVFDKALVLC QMHDFQDGVL YLYEQGKLFQ QIMHYHMQHE
710 720 730 740 750
QYRQVISVCE RHGEQDPSLW EQALSYFARK EEDCKEYVAA VLKHIENKNL
760 770 780 790 800
MPPLLVVQTL AHNSTATLSV IRDYLVQKLQ KQSQQIAQDE LRVRRYREET
810 820 830 840 850
TRIRQEIQEL KASPKIFQKT KCSICNSALE LPSVHFLCGH SFHQHCFESY
860 870 880 890 900
SESDADCPTC LPENRKVMDM IRAQEQKRDL HDQFQHQLRC SNDSFSVIAD
910 920 930 940
YFGRGVFNKL TLLTDPPTAR LTSSLEAGLQ RDLLMHSRRG T
Length:941
Mass (Da):107,837
Last modified:March 1, 2001 - v1
Checksum:iC1F8E538ED1B56DB
GO

Sequence cautioni

The sequence AAG23761 differs from that shown. Reason: Frameshift at positions 439 and 924.Curated
The sequence BAB15320 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti635 – 636AH → VI in BAA95163 (PubMed:11382755).Curated2
Sequence conflicti871I → T in BAB15320 (PubMed:14702039).Curated1
Sequence conflicti889R → K in BAA95163 (PubMed:11382755).Curated1
Sequence conflicti889R → K in AAG23761 (PubMed:15498874).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_059813770V → I. Corresponds to variant dbSNP:rs11558589Ensembl.1
Natural variantiVAR_076393846C → G in HLD12. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF308800 mRNA. Translation: AAG34677.1.
AB027508 mRNA. Translation: BAA95163.2.
BC012051 mRNA. Translation: AAH12051.2.
BC065563 mRNA. Translation: AAH65563.1.
AF258558 mRNA. Translation: AAG23761.1. Frameshift.
AK026012 mRNA. Translation: BAB15320.1. Different initiation.
CCDSiCCDS73404.1.
RefSeqiNP_001277114.1. NM_001290185.1.
NP_068375.3. NM_021729.5.
UniGeneiHs.234282.

Genome annotation databases

EnsembliENST00000620429; ENSP00000479680; ENSG00000160695.
GeneIDi55823.
KEGGihsa:55823.
UCSCiuc058ier.1. human.

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiVPS11_HUMAN
AccessioniPrimary (citable) accession number: Q9H270
Secondary accession number(s): Q8WY89
, Q96EP8, Q9H6D9, Q9HCS6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2002
Last sequence update: March 1, 2001
Last modified: November 22, 2017
This is version 165 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families