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Protein

Syndetin

Gene

VPS50

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

Functioni

Acts as component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane. Within the EARP complex, required to tether the complex to recycling endosomes. Not involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN).1 Publication

GO - Molecular functioni

  • SNARE binding Source: MGI

GO - Biological processi

  • endocytic recycling Source: UniProtKB
  • protein transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Protein transport, Transport

Names & Taxonomyi

Protein namesi
Recommended name:
Syndetin1 Publication
Alternative name(s):
Coiled-coil domain-containing protein 132Curated
EARP/GARPII complex subunit VPS50Imported
Gene namesi
Name:VPS50Imported
Synonyms:CCDC132, KIAA18611 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 7

Organism-specific databases

HGNCiHGNC:25956. VPS50.

Subcellular locationi

GO - Cellular componenti

  • EARP complex Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • membrane Source: UniProtKB
  • recycling endosome Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Endosome

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000004766.
PharmGKBiPA162381332.

Polymorphism and mutation databases

BioMutaiCCDC132.
DMDMi160019079.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003072651 – 964SyndetinAdd BLAST964

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei15PhosphoserineCombined sources1
Modified residuei494PhosphoserineCombined sources1
Modified residuei498PhosphoserineCombined sources1
Modified residuei559PhosphoserineCombined sources1
Modified residuei561PhosphoserineCombined sources1
Cross-linki963Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Cross-linki963Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96JG6.
MaxQBiQ96JG6.
PaxDbiQ96JG6.
PeptideAtlasiQ96JG6.
PRIDEiQ96JG6.

PTM databases

iPTMnetiQ96JG6.
PhosphoSitePlusiQ96JG6.

Expressioni

Tissue specificityi

Ubiquitous, with higher expression in brain and skeletal muscle.1 Publication

Gene expression databases

BgeeiENSG00000004766.
CleanExiHS_CCDC132.
ExpressionAtlasiQ96JG6. baseline and differential.
GenevisibleiQ96JG6. HS.

Organism-specific databases

HPAiHPA026679.

Interactioni

Subunit structurei

Component of the endosome-associated retrograde protein (EARP) complex, composed of VPS51, VPS52, VPS53 and VPS50/Syndetin (PubMed:25799061). Interacts with TSSC1 (By similarity).By similarity1 Publication

GO - Molecular functioni

  • SNARE binding Source: MGI

Protein-protein interaction databases

BioGridi120750. 31 interactors.
DIPiDIP-61628N.
IntActiQ96JG6. 20 interactors.
STRINGi9606.ENSP00000307666.

Structurei

3D structure databases

ProteinModelPortaliQ96JG6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili82 – 105Sequence analysisAdd BLAST24
Coiled coili216 – 244Sequence analysisAdd BLAST29

Sequence similaritiesi

Belongs to the syndetin family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2939. Eukaryota.
ENOG410XS88. LUCA.
GeneTreeiENSGT00390000003442.
HOGENOMiHOG000230787.
HOVERGENiHBG075377.
InParanoidiQ96JG6.
OMAiENDMEQF.
OrthoDBiEOG091G01I8.
PhylomeDBiQ96JG6.
TreeFamiTF106152.

Family and domain databases

InterProiIPR019514. DUF2451_C.
IPR019515. VPS54_N.
[Graphical view]
PfamiPF10474. DUF2451. 1 hit.
PF10475. Vps54_N. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96JG6-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MQKIKSLMTR QGLKSPQESL SDLGAIESLR VPGKEEFREL REQPSDPQAE
60 70 80 90 100
QELINSIEQV YFSVDSFDIV KYELEKLPPV LNLQELEAYR DKLKQQQAAV
110 120 130 140 150
SKKVADLILE KQPAYVKELE RVTSLQTGLQ LAAVICTNGR RHLNIAKEGF
160 170 180 190 200
TQASLGLLAN QRKRQLLIGL LKSLRTIKTL QRTDVRLSEM LEEEDYPGAI
210 220 230 240 250
QLCLECQKAA STFKHYSCIS ELNSKLQDTL EQIEEQLDVA LSKICKNFDI
260 270 280 290 300
NHYTKVQQAY RLLGKTQTAM DQLHMHFTQA IHNTVFQVVL GYVELCAGNT
310 320 330 340 350
DTKFQKLQYK DLCTHVTPDS YIPCLADLCK ALWEVMLSYY RTMEWHEKHD
360 370 380 390 400
NEDTASASEG SNMIGTEETN FDRGYIKKKL EHGLTRIWQD VQLKVKTYLL
410 420 430 440 450
GTDLSIFKYD DFIFVLDIIS RLMQVGEEFC GSKSEVLQES IRKQSVNYFK
460 470 480 490 500
NYHRTRLDEL RMFLENETWE LCPVKSNFSI LQLHEFKFME QSRSPSVSPS
510 520 530 540 550
KQPVSTSSKT VTLFEQYCSG GNPFEIQANH KDEETEDVLA SNGYESDEQE
560 570 580 590 600
KSAYQEYDSD SDVPEELKRD YVDEQTGDGP VKSVSRETLK SRKKSDYSLN
610 620 630 640 650
KVNAPILTNT TLNVIRLVGK YMQMMNILKP IAFDVIHFMS QLFDYYLYAI
660 670 680 690 700
YTFFGRNDSL ESTGLGLSSS RLRTTLNRIQ ESLIDLEVSA DPTATLTAAE
710 720 730 740 750
ERKEKVPSPH LSHLVVLTSG DTLYGLAERV VATESLVFLA EQFEFLQPHL
760 770 780 790 800
DAVMPAVKKP FLQQFYSQTV STASELRKPI YWIVAGKALD YEQMLLLMAN
810 820 830 840 850
VKWDVKEIMS QHNIYVDALL KEFEQFNRRL NEVSKRVRIP LPVSNILWEH
860 870 880 890 900
CIRLANRTIV EGYANVKKCS NEGRALMQLD FQQFLMKLEK LTDIRPIPDK
910 920 930 940 950
EFVETYIKAY YLTENDMERW IKEHREYSTK QLTNLVNVCL GSHINKKARQ
960
KLLAAIDDID RPKR
Length:964
Mass (Da):111,174
Last modified:October 23, 2007 - v3
Checksum:i2C748490DDBCBAD5
GO
Isoform 2 (identifier: Q96JG6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     315-327: HVTPDSYIPCLAD → VCSDLITIHISLL
     328-964: Missing.

Show »
Length:327
Mass (Da):37,259
Checksum:iB2E9D603F5DEBFE2
GO
Isoform 3 (identifier: Q96JG6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-34: MQKIKSLMTRQGLKSPQESLSDLGAIESLRVPGK → MLTL

Note: No experimental confirmation available.
Show »
Length:934
Mass (Da):107,923
Checksum:i0BF781F226FB22C2
GO

Sequence cautioni

The sequence BAB15701 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAB47490 differs from that shown. Reason: Frameshift at position 2.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti96Q → H in BAG54334 (PubMed:14702039).Curated1
Sequence conflicti670Missing in BAB15701 (PubMed:14702039).Curated1
Sequence conflicti812H → Y in BAB15701 (PubMed:14702039).Curated1
Sequence conflicti926E → K in BAB15701 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0455721 – 34MQKIK…RVPGK → MLTL in isoform 3. 1 PublicationAdd BLAST34
Alternative sequenceiVSP_028658315 – 327HVTPD…PCLAD → VCSDLITIHISLL in isoform 2. 1 PublicationAdd BLAST13
Alternative sequenceiVSP_028659328 – 964Missing in isoform 2. 1 PublicationAdd BLAST637

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB058764 mRNA. Translation: BAB47490.2. Frameshift.
AB100163 mRNA. Translation: BAI52922.1.
AK027234 mRNA. Translation: BAB15701.1. Different initiation.
AK126478 mRNA. Translation: BAG54334.1.
AC002379 Genomic DNA. No translation available.
AC002453 Genomic DNA. Translation: AAS02023.1.
CH236949 Genomic DNA. Translation: EAL24143.1.
CH471091 Genomic DNA. Translation: EAW76816.1.
CH471091 Genomic DNA. Translation: EAW76818.1.
BC108708 mRNA. Translation: AAI08709.1.
BC017888 mRNA. Translation: AAH17888.1.
BC132740 mRNA. Translation: AAI32741.1.
BC132742 mRNA. Translation: AAI32743.1.
CCDSiCCDS43617.1. [Q96JG6-1]
CCDS5630.1. [Q96JG6-2]
CCDS59065.1. [Q96JG6-3]
RefSeqiNP_001244927.1. NM_001257998.1. [Q96JG6-3]
NP_060137.2. NM_017667.3. [Q96JG6-1]
NP_078829.1. NM_024553.2. [Q96JG6-2]
UniGeneiHs.202424.

Genome annotation databases

EnsembliENST00000251739; ENSP00000251739; ENSG00000004766. [Q96JG6-2]
ENST00000305866; ENSP00000307666; ENSG00000004766. [Q96JG6-1]
ENST00000544910; ENSP00000443104; ENSG00000004766. [Q96JG6-3]
GeneIDi55610.
KEGGihsa:55610.
UCSCiuc003umn.4. human. [Q96JG6-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB058764 mRNA. Translation: BAB47490.2. Frameshift.
AB100163 mRNA. Translation: BAI52922.1.
AK027234 mRNA. Translation: BAB15701.1. Different initiation.
AK126478 mRNA. Translation: BAG54334.1.
AC002379 Genomic DNA. No translation available.
AC002453 Genomic DNA. Translation: AAS02023.1.
CH236949 Genomic DNA. Translation: EAL24143.1.
CH471091 Genomic DNA. Translation: EAW76816.1.
CH471091 Genomic DNA. Translation: EAW76818.1.
BC108708 mRNA. Translation: AAI08709.1.
BC017888 mRNA. Translation: AAH17888.1.
BC132740 mRNA. Translation: AAI32741.1.
BC132742 mRNA. Translation: AAI32743.1.
CCDSiCCDS43617.1. [Q96JG6-1]
CCDS5630.1. [Q96JG6-2]
CCDS59065.1. [Q96JG6-3]
RefSeqiNP_001244927.1. NM_001257998.1. [Q96JG6-3]
NP_060137.2. NM_017667.3. [Q96JG6-1]
NP_078829.1. NM_024553.2. [Q96JG6-2]
UniGeneiHs.202424.

3D structure databases

ProteinModelPortaliQ96JG6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120750. 31 interactors.
DIPiDIP-61628N.
IntActiQ96JG6. 20 interactors.
STRINGi9606.ENSP00000307666.

PTM databases

iPTMnetiQ96JG6.
PhosphoSitePlusiQ96JG6.

Polymorphism and mutation databases

BioMutaiCCDC132.
DMDMi160019079.

Proteomic databases

EPDiQ96JG6.
MaxQBiQ96JG6.
PaxDbiQ96JG6.
PeptideAtlasiQ96JG6.
PRIDEiQ96JG6.

Protocols and materials databases

DNASUi55610.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000251739; ENSP00000251739; ENSG00000004766. [Q96JG6-2]
ENST00000305866; ENSP00000307666; ENSG00000004766. [Q96JG6-1]
ENST00000544910; ENSP00000443104; ENSG00000004766. [Q96JG6-3]
GeneIDi55610.
KEGGihsa:55610.
UCSCiuc003umn.4. human. [Q96JG6-1]

Organism-specific databases

CTDi55610.
GeneCardsiCCDC132.
H-InvDBHIX0006848.
HGNCiHGNC:25956. VPS50.
HPAiHPA026679.
MIMi616465. gene.
neXtProtiNX_Q96JG6.
OpenTargetsiENSG00000004766.
PharmGKBiPA162381332.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2939. Eukaryota.
ENOG410XS88. LUCA.
GeneTreeiENSGT00390000003442.
HOGENOMiHOG000230787.
HOVERGENiHBG075377.
InParanoidiQ96JG6.
OMAiENDMEQF.
OrthoDBiEOG091G01I8.
PhylomeDBiQ96JG6.
TreeFamiTF106152.

Miscellaneous databases

ChiTaRSiCCDC132. human.
GeneWikiiFLJ20097_/_CCDC132.
GenomeRNAii55610.
PROiQ96JG6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000004766.
CleanExiHS_CCDC132.
ExpressionAtlasiQ96JG6. baseline and differential.
GenevisibleiQ96JG6. HS.

Family and domain databases

InterProiIPR019514. DUF2451_C.
IPR019515. VPS54_N.
[Graphical view]
PfamiPF10474. DUF2451. 1 hit.
PF10475. Vps54_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVPS50_HUMAN
AccessioniPrimary (citable) accession number: Q96JG6
Secondary accession number(s): B3KX22
, D1MQ00, F5H5U7, Q75N07, Q8WVK3, Q9H5C6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: October 23, 2007
Last modified: November 2, 2016
This is version 105 of the entry and version 3 of the sequence. [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

Miscellaneous

Was named 'syndetin' after the Greek 'syndeo', which means 'connect' or 'tether'.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.