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Protein

Syndetin

Gene

VPS50

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Miscellaneous

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

GO - Molecular functioni

  • SNARE binding Source: MGI

GO - Biological processi

Keywordsi

Biological processProtein 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

EuPathDBiHostDB:ENSG00000004766.15
HGNCiHGNC:25956 VPS50
MIMi616465 gene
neXtProtiNX_Q96JG6

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

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); alternateCombined sources
Cross-linki963Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96JG6
MaxQBiQ96JG6
PaxDbiQ96JG6
PeptideAtlasiQ96JG6
PRIDEiQ96JG6
ProteomicsDBi76956
76957 [Q96JG6-2]

PTM databases

iPTMnetiQ96JG6
PhosphoSitePlusiQ96JG6

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000004766 Expressed in 203 organ(s), highest expression level in stomach
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, PubMed:27440922). The EARP complex interacts with EIPR1 (PubMed:27440922).2 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi120750, 66 interactors
CORUMiQ96JG6
DIPiDIP-61628N
IntActiQ96JG6, 27 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
OMAiAKVKWDV
OrthoDBiEOG091G01I8
PhylomeDBiQ96JG6
TreeFamiTF106152

Family and domain databases

InterProiView protein in InterPro
IPR019514 Syndetin_C
IPR040047 VPS50
IPR019515 VPS54_N
PANTHERiPTHR13258 PTHR13258, 1 hit
PfamiView protein in Pfam
PF10474 DUF2451, 1 hit
PF10475 Vps54_N, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y7Q2H0Y7Q2_HUMAN
Syndetin
VPS50
469Annotation score:
C9JA29C9JA29_HUMAN
Syndetin
VPS50
189Annotation score:
H7BZP1H7BZP1_HUMAN
Syndetin
VPS50
155Annotation score:
F8WDT1F8WDT1_HUMAN
Syndetin
VPS50
37Annotation score:
F2Z3F0F2Z3F0_HUMAN
Syndetin
VPS50
39Annotation score:

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

Similar proteinsi

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, 66 interactors
CORUMiQ96JG6
DIPiDIP-61628N
IntActiQ96JG6, 27 interactors
STRINGi9606.ENSP00000307666

PTM databases

iPTMnetiQ96JG6
PhosphoSitePlusiQ96JG6

Polymorphism and mutation databases

BioMutaiCCDC132
DMDMi160019079

Proteomic databases

EPDiQ96JG6
MaxQBiQ96JG6
PaxDbiQ96JG6
PeptideAtlasiQ96JG6
PRIDEiQ96JG6
ProteomicsDBi76956
76957 [Q96JG6-2]

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
EuPathDBiHostDB:ENSG00000004766.15
GeneCardsiVPS50
H-InvDBiHIX0006848
HGNCiHGNC:25956 VPS50
HPAiHPA026679
MIMi616465 gene
neXtProtiNX_Q96JG6
OpenTargetsiENSG00000004766
PharmGKBiPA162381332
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2939 Eukaryota
ENOG410XS88 LUCA
GeneTreeiENSGT00390000003442
HOGENOMiHOG000230787
HOVERGENiHBG075377
InParanoidiQ96JG6
OMAiAKVKWDV
OrthoDBiEOG091G01I8
PhylomeDBiQ96JG6
TreeFamiTF106152

Miscellaneous databases

ChiTaRSiVPS50 human
GeneWikiiFLJ20097_/_CCDC132
GenomeRNAii55610
PROiPR:Q96JG6
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000004766 Expressed in 203 organ(s), highest expression level in stomach
CleanExiHS_CCDC132
ExpressionAtlasiQ96JG6 baseline and differential
GenevisibleiQ96JG6 HS

Family and domain databases

InterProiView protein in InterPro
IPR019514 Syndetin_C
IPR040047 VPS50
IPR019515 VPS54_N
PANTHERiPTHR13258 PTHR13258, 1 hit
PfamiView protein in Pfam
PF10474 DUF2451, 1 hit
PF10475 Vps54_N, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiVPS50_HUMAN
AccessioniPrimary (citable) accession number: Q96JG6
Secondary accession number(s): B3KX22
, D1MQ00, F5H5U7, Q75N07, Q8WVK3, Q9H5C6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 23, 2007
Last sequence update: October 23, 2007
Last modified: November 7, 2018
This is version 118 of the entry and version 3 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 7
    Human chromosome 7: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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