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Protein

Synaptotagmin-1

Gene

Syt1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. It binds acidic phospholipids with a specificity that requires the presence of both an acidic head group and a diacyl backbone. A Ca2+-dependent interaction between synaptotagmin and putative receptors for activated protein kinase C has also been reported. It can bind to at least three additional proteins in a Ca2+-independent manner; these are neurexins, syntaxin and AP2. Plays a role in dendrite formation by melanocytes.By similarity

Cofactori

Ca2+2 PublicationsNote: Binds 3 Ca2+ ions per subunit. The ions are bound to the C2 domains.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi171Calcium 2; via carbonyl oxygen1 Publication1
Metal bindingi172Calcium 11 Publication1
Metal bindingi172Calcium 21 Publication1
Metal bindingi178Calcium 11 Publication1
Metal bindingi230Calcium 11 Publication1
Metal bindingi230Calcium 21 Publication1
Metal bindingi231Calcium 1; via carbonyl oxygen1 Publication1
Metal bindingi232Calcium 11 Publication1
Metal bindingi232Calcium 21 Publication1
Metal bindingi232Calcium 31 Publication1
Metal bindingi235Calcium 31 Publication1
Metal bindingi236Calcium 3; via carbonyl oxygen1 Publication1
Metal bindingi238Calcium 21 Publication1
Metal bindingi238Calcium 31 Publication1

GO - Molecular functioni

  • calcium-dependent phospholipid binding Source: BHF-UCL
  • calcium-dependent protein binding Source: ParkinsonsUK-UCL
  • calcium ion binding Source: RGD
  • calmodulin binding Source: RGD
  • clathrin binding Source: BHF-UCL
  • phosphatidylinositol-4,5-bisphosphate binding Source: ParkinsonsUK-UCL
  • phosphatidylserine binding Source: ParkinsonsUK-UCL
  • phospholipid binding Source: ParkinsonsUK-UCL
  • protein C-terminus binding Source: RGD
  • protein heterodimerization activity Source: ParkinsonsUK-UCL
  • protein homodimerization activity Source: ParkinsonsUK-UCL
  • SNARE binding Source: ParkinsonsUK-UCL
  • syntaxin-1 binding Source: ParkinsonsUK-UCL
  • syntaxin-3 binding Source: ParkinsonsUK-UCL
  • syntaxin binding Source: BHF-UCL

GO - Biological processi

  • brain development Source: RGD
  • calcium ion regulated exocytosis Source: RGD
  • calcium ion-regulated exocytosis of neurotransmitter Source: GO_Central
  • cellular response to calcium ion Source: ParkinsonsUK-UCL
  • detection of calcium ion Source: RGD
  • fast, calcium ion-dependent exocytosis of neurotransmitter Source: ParkinsonsUK-UCL
  • positive regulation of calcium ion-dependent exocytosis Source: RGD
  • positive regulation of dendrite extension Source: Ensembl
  • positive regulation of synaptic transmission Source: ParkinsonsUK-UCL
  • positive regulation of vesicle fusion Source: ParkinsonsUK-UCL
  • protein heterooligomerization Source: ParkinsonsUK-UCL
  • protein homooligomerization Source: ParkinsonsUK-UCL
  • regulation of calcium ion-dependent exocytosis Source: ParkinsonsUK-UCL
  • regulation of regulated secretory pathway Source: ParkinsonsUK-UCL
  • regulation of synaptic transmission, glutamatergic Source: ParkinsonsUK-UCL
  • response to calcium ion Source: RGD
  • synaptic vesicle endocytosis Source: GO_Central
  • synaptic vesicle exocytosis Source: RGD
  • vesicle docking Source: RGD
Complete GO annotation...

Keywords - Biological processi

Differentiation

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

ReactomeiR-RNO-181430. Norepinephrine Neurotransmitter Release Cycle.
R-RNO-210500. Glutamate Neurotransmitter Release Cycle.
R-RNO-264642. Acetylcholine Neurotransmitter Release Cycle.
R-RNO-8856825. Cargo recognition for clathrin-mediated endocytosis.
R-RNO-8856828. Clathrin-mediated endocytosis.
R-RNO-888590. GABA synthesis, release, reuptake and degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptotagmin-1
Alternative name(s):
Synaptotagmin I
Short name:
SytI
p65
Gene namesi
Name:Syt1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 7

Organism-specific databases

RGDi3803. Syt1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 57VesicularSequence analysisAdd BLAST57
Transmembranei58 – 79HelicalSequence analysisAdd BLAST22
Topological domaini80 – 421CytoplasmicSequence analysisAdd BLAST342

GO - Cellular componenti

  • cell junction Source: UniProtKB-KW
  • chromaffin granule membrane Source: UniProtKB-SubCell
  • cytoplasm Source: MGI
  • dense core granule Source: RGD
  • excitatory synapse Source: BHF-UCL
  • Golgi apparatus Source: Ensembl
  • integral component of membrane Source: UniProtKB-KW
  • intracellular organelle Source: RGD
  • neuron projection terminus Source: ParkinsonsUK-UCL
  • plasma membrane Source: BHF-UCL
  • presynaptic membrane Source: Ensembl
  • secretory granule Source: RGD
  • synaptic vesicle Source: BHF-UCL
  • synaptic vesicle membrane Source: RGD
  • terminal bouton Source: ParkinsonsUK-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasm, Cytoplasmic vesicle, Membrane, Synapse

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi233R → Q: Impaired Ca(2+)-affinity. 1 Publication1
Mutagenesisi367I → T: Slows synaptic vesicle fusion kinetics and impairs the kinetics of synaptic vesicle endocytosis. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001839401 – 421Synaptotagmin-1Add BLAST421

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi24N-linked (GlcNAc...)1
Lipidationi74S-palmitoyl cysteine1 Publication1
Lipidationi75S-palmitoyl cysteine1 Publication1
Lipidationi77S-palmitoyl cysteine1 Publication1
Lipidationi79S-palmitoyl cysteine1 Publication1
Lipidationi82S-palmitoyl cysteine1 Publication1
Modified residuei125PhosphothreonineBy similarity1
Modified residuei128PhosphothreonineCombined sources1
Modified residuei229PhosphotyrosineBy similarity1
Modified residuei264PhosphoserineBy similarity1
Modified residuei342PhosphoserineCombined sources1
Modified residuei344PhosphoserineCombined sources1

Keywords - PTMi

Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein

Proteomic databases

PaxDbiP21707.
PRIDEiP21707.

PTM databases

iPTMnetiP21707.
PhosphoSitePlusiP21707.
SwissPalmiP21707.

Expressioni

Tissue specificityi

Predominantly expressed in rostral, phylogenetically younger brain regions, and in some endocrine tissues.

Gene expression databases

BgeeiENSRNOG00000006426.
GenevisibleiP21707. RN.

Interactioni

Subunit structurei

Homotetramer (Probable). Interacts with SCAMP5 and STON2. Forms a complex with SV2B, syntaxin 1 and SNAP25 (By similarity). Interacts with RIMS1. Interacts with SV2A, SV2B and SV2C.By similarityCurated3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-458098,EBI-458098
Ap2a2P184845EBI-458098,EBI-539360
Cacna1bQ022942EBI-458098,EBI-540038
Scn1bQ009542EBI-458098,EBI-2619363
Scn2aP047752EBI-458098,EBI-2619448
STON2Q8WXE92EBI-458098,EBI-539742From a different organism.
Sv2aQ025632EBI-458098,EBI-466194

GO - Molecular functioni

  • calcium-dependent protein binding Source: ParkinsonsUK-UCL
  • calmodulin binding Source: RGD
  • clathrin binding Source: BHF-UCL
  • protein C-terminus binding Source: RGD
  • protein heterodimerization activity Source: ParkinsonsUK-UCL
  • protein homodimerization activity Source: ParkinsonsUK-UCL
  • SNARE binding Source: ParkinsonsUK-UCL
  • syntaxin-1 binding Source: ParkinsonsUK-UCL
  • syntaxin-3 binding Source: ParkinsonsUK-UCL
  • syntaxin binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi247745. 1 interactor.
DIPiDIP-29064N.
IntActiP21707. 17 interactors.
MINTiMINT-4542559.
STRINGi10116.ENSRNOP00000049624.

Structurei

Secondary structure

1421
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi144 – 152Combined sources9
Turni153 – 156Combined sources4
Beta strandi157 – 166Combined sources10
Helixi172 – 174Combined sources3
Beta strandi179 – 187Combined sources9
Beta strandi205 – 212Combined sources8
Helixi216 – 219Combined sources4
Beta strandi223 – 230Combined sources8
Beta strandi233 – 235Combined sources3
Beta strandi238 – 246Combined sources9
Helixi247 – 249Combined sources3
Beta strandi256 – 261Combined sources6
Beta strandi275 – 283Combined sources9
Turni284 – 287Combined sources4
Beta strandi288 – 298Combined sources11
Beta strandi310 – 318Combined sources9
Beta strandi321 – 327Combined sources7
Beta strandi338 – 346Combined sources9
Helixi349 – 354Combined sources6
Beta strandi356 – 363Combined sources8
Beta strandi366 – 368Combined sources3
Beta strandi371 – 379Combined sources9
Helixi384 – 395Combined sources12
Beta strandi396 – 399Combined sources4
Beta strandi401 – 406Combined sources6
Helixi410 – 417Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BYNNMR-A140-267[»]
1K5WNMR-A270-421[»]
1RSYX-ray1.90A132-266[»]
1TJMX-ray1.18A271-421[»]
1TJXX-ray1.04A271-421[»]
1UOVX-ray1.65A271-421[»]
1UOWX-ray1.04A271-421[»]
2YOAX-ray1.50A/B271-421[»]
4WEEX-ray0.89A140-266[»]
5CCGX-ray3.50E/F/K141-421[»]
5CCHX-ray3.60E/F141-421[»]
5CCIX-ray4.10E/F141-421[»]
5CCJX-ray1.65A/B/C/D271-421[»]
5KJ7X-ray3.50E/F/K141-419[»]
5KJ8X-ray4.10E/F/K141-419[»]
ProteinModelPortaliP21707.
SMRiP21707.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21707.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini143 – 244C2 1PROSITE-ProRule annotationAdd BLAST102
Domaini274 – 377C2 2PROSITE-ProRule annotationAdd BLAST104

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni135 – 381Phospholipid bindingCuratedAdd BLAST247

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi80 – 119Lys-richAdd BLAST40

Domaini

The first C2 domain mediates Ca2+-dependent phospholipid binding.2 Publications
The second C2 domain mediates interaction with SV2A and probably with STN2.1 Publication

Sequence similaritiesi

Belongs to the synaptotagmin family.Curated
Contains 2 C2 domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IT3Q. Eukaryota.
ENOG410Z15P. LUCA.
GeneTreeiENSGT00760000118973.
HOGENOMiHOG000232127.
HOVERGENiHBG005010.
InParanoidiP21707.
KOiK15290.
OMAiGEFKVAM.
OrthoDBiEOG091G0XMQ.
PhylomeDBiP21707.
TreeFamiTF315600.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR015428. Synaptotagmin1.
[Graphical view]
PANTHERiPTHR10024:SF239. PTHR10024:SF239. 1 hit.
PfamiPF00168. C2. 2 hits.
[Graphical view]
PRINTSiPR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
PROSITEiPS50004. C2. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P21707-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVSASHPEAL AAPVTTVATL VPHNATEPAS PGEGKEDAFS KLKQKFMNEL
60 70 80 90 100
HKIPLPPWAL IAIAIVAVLL VVTCCFCVCK KCLFKKKNKK KGKEKGGKNA
110 120 130 140 150
INMKDVKDLG KTMKDQALKD DDAETGLTDG EEKEEPKEEE KLGKLQYSLD
160 170 180 190 200
YDFQNNQLLV GIIQAAELPA LDMGGTSDPY VKVFLLPDKK KKFETKVHRK
210 220 230 240 250
TLNPVFNEQF TFKVPYSELG GKTLVMAVYD FDRFSKHDII GEFKVPMNTV
260 270 280 290 300
DFGHVTEEWR DLQSAEKEEQ EKLGDICFSL RYVPTAGKLT VVILEAKNLK
310 320 330 340 350
KMDVGGLSDP YVKIHLMQNG KRLKKKKTTI KKNTLNPYYN ESFSFEVPFE
360 370 380 390 400
QIQKVQVVVT VLDYDKIGKN DAIGKVFVGY NSTGAELRHW SDMLANPRRP
410 420
IAQWHTLQVE EEVDAMLAVK K
Length:421
Mass (Da):47,399
Last modified:May 2, 2006 - v3
Checksum:i06CE28F04C97A722
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti188D → E in CAA36981 (PubMed:2333096).Curated1
Sequence conflicti374G → D in CAA36981 (PubMed:2333096).Curated1
Sequence conflicti393M → I in CAA36981 (PubMed:2333096).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52772 mRNA. Translation: CAA36981.1.
AJ617615 mRNA. Translation: CAE85101.1.
DQ181550 mRNA. Translation: ABA00482.1.
PIRiS09595.
RefSeqiNP_001028852.2. NM_001033680.2.
XP_017450168.1. XM_017594679.1.
UniGeneiRn.216272.

Genome annotation databases

EnsembliENSRNOT00000048880; ENSRNOP00000049624; ENSRNOG00000006426.
ENSRNOT00000088950; ENSRNOP00000069194; ENSRNOG00000006426.
GeneIDi25716.
KEGGirno:25716.
UCSCiRGD:3803. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52772 mRNA. Translation: CAA36981.1.
AJ617615 mRNA. Translation: CAE85101.1.
DQ181550 mRNA. Translation: ABA00482.1.
PIRiS09595.
RefSeqiNP_001028852.2. NM_001033680.2.
XP_017450168.1. XM_017594679.1.
UniGeneiRn.216272.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BYNNMR-A140-267[»]
1K5WNMR-A270-421[»]
1RSYX-ray1.90A132-266[»]
1TJMX-ray1.18A271-421[»]
1TJXX-ray1.04A271-421[»]
1UOVX-ray1.65A271-421[»]
1UOWX-ray1.04A271-421[»]
2YOAX-ray1.50A/B271-421[»]
4WEEX-ray0.89A140-266[»]
5CCGX-ray3.50E/F/K141-421[»]
5CCHX-ray3.60E/F141-421[»]
5CCIX-ray4.10E/F141-421[»]
5CCJX-ray1.65A/B/C/D271-421[»]
5KJ7X-ray3.50E/F/K141-419[»]
5KJ8X-ray4.10E/F/K141-419[»]
ProteinModelPortaliP21707.
SMRiP21707.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi247745. 1 interactor.
DIPiDIP-29064N.
IntActiP21707. 17 interactors.
MINTiMINT-4542559.
STRINGi10116.ENSRNOP00000049624.

PTM databases

iPTMnetiP21707.
PhosphoSitePlusiP21707.
SwissPalmiP21707.

Proteomic databases

PaxDbiP21707.
PRIDEiP21707.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000048880; ENSRNOP00000049624; ENSRNOG00000006426.
ENSRNOT00000088950; ENSRNOP00000069194; ENSRNOG00000006426.
GeneIDi25716.
KEGGirno:25716.
UCSCiRGD:3803. rat.

Organism-specific databases

CTDi6857.
RGDi3803. Syt1.

Phylogenomic databases

eggNOGiENOG410IT3Q. Eukaryota.
ENOG410Z15P. LUCA.
GeneTreeiENSGT00760000118973.
HOGENOMiHOG000232127.
HOVERGENiHBG005010.
InParanoidiP21707.
KOiK15290.
OMAiGEFKVAM.
OrthoDBiEOG091G0XMQ.
PhylomeDBiP21707.
TreeFamiTF315600.

Enzyme and pathway databases

ReactomeiR-RNO-181430. Norepinephrine Neurotransmitter Release Cycle.
R-RNO-210500. Glutamate Neurotransmitter Release Cycle.
R-RNO-264642. Acetylcholine Neurotransmitter Release Cycle.
R-RNO-8856825. Cargo recognition for clathrin-mediated endocytosis.
R-RNO-8856828. Clathrin-mediated endocytosis.
R-RNO-888590. GABA synthesis, release, reuptake and degradation.

Miscellaneous databases

EvolutionaryTraceiP21707.
PROiP21707.

Gene expression databases

BgeeiENSRNOG00000006426.
GenevisibleiP21707. RN.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR015428. Synaptotagmin1.
[Graphical view]
PANTHERiPTHR10024:SF239. PTHR10024:SF239. 1 hit.
PfamiPF00168. C2. 2 hits.
[Graphical view]
PRINTSiPR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
PROSITEiPS50004. C2. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYT1_RAT
AccessioniPrimary (citable) accession number: P21707
Secondary accession number(s): Q3S2E6, Q707P5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: May 2, 2006
Last modified: November 30, 2016
This is version 173 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.