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P21707 (SYT1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 146. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Synaptotagmin-1
Alternative name(s):
Synaptotagmin I
Short name=SytI
p65
Gene names
Name:Syt1
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length421 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Cofactor

Binds 3 calcium ions per subunit. The ions are bound to the C2 domains.

Subunit structure

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. Ref.5 Ref.6 Ref.8

Subcellular location

Cytoplasmic vesiclesecretory vesiclesynaptic vesicle membrane; Single-pass membrane protein. Cytoplasmic vesiclesecretory vesiclechromaffin granule membrane; Single-pass membrane protein. Cytoplasm. Note: Synaptic vesicles and chromaffin granules.

Tissue specificity

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

Domain

The first C2 domain mediates Ca2+-dependent phospholipid binding. Ref.5

The second C2 domain mediates interaction with SV2A and probably with STN2. Ref.5

Sequence similarities

Belongs to the synaptotagmin family.

Contains 2 C2 domains.

Ontologies

Keywords
   Cellular componentCell junction
Cytoplasm
Cytoplasmic vesicle
Membrane
Synapse
   DomainRepeat
Transmembrane
Transmembrane helix
   LigandCalcium
Metal-binding
   PTMGlycoprotein
Lipoprotein
Palmitate
Phosphoprotein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processcalcium ion-dependent exocytosis

Traceable author statement Ref.1. Source: RGD

detection of calcium ion

Inferred from direct assay PubMed 22229667. Source: RGD

positive regulation of calcium ion-dependent exocytosis

Inferred from direct assay PubMed 21551071. Source: RGD

positive regulation of vesicle fusion

Inferred from direct assay PubMed 18508778. Source: RGD

regulation of calcium ion-dependent exocytosis

Inferred from mutant phenotype PubMed 11751925PubMed 17686463. Source: RGD

response to calcium ion

Inferred from direct assay PubMed 18508778. Source: RGD

synaptic vesicle exocytosis

Traceable author statement Ref.1. Source: RGD

vesicle docking

Inferred from direct assay PubMed 22229667. Source: RGD

   Cellular_componentcell junction

Inferred from electronic annotation. Source: UniProtKB-KW

chromaffin granule membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

cytoplasm

Inferred from direct assay PubMed 10967100. Source: MGI

dense core granule

Inferred from direct assay PubMed 22366033. Source: MGI

excitatory synapse

Inferred from direct assay PubMed 19730411. Source: BHF-UCL

integral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

intracellular organelle

Inferred from direct assay PubMed 10340764. Source: RGD

neuron projection

Inferred from electronic annotation. Source: Ensembl

plasma membrane

Inferred from direct assay PubMed 18179895. Source: BHF-UCL

presynaptic membrane

Inferred from electronic annotation. Source: Ensembl

secretory granule

Inferred from direct assay PubMed 15015935. Source: RGD

synaptic vesicle

Inferred from direct assay PubMed 18179895. Source: BHF-UCL

synaptic vesicle membrane

Traceable author statement Ref.1. Source: RGD

   Molecular_functionSNARE binding

Inferred from direct assay PubMed 18508778PubMed 19132534PubMed 22711810. Source: RGD

calcium ion binding

Inferred from direct assay PubMed 15340165PubMed 22447935. Source: RGD

calcium-dependent phospholipid binding

Inferred from direct assay PubMed 7791877. Source: BHF-UCL

calcium-dependent protein binding

Inferred from direct assay PubMed 22711810. Source: RGD

calmodulin binding

Inferred from direct assay Ref.1. Source: RGD

clathrin binding

Inferred from direct assay PubMed 7791877. Source: BHF-UCL

identical protein binding

Inferred from physical interaction PubMed 9830048. Source: IntAct

phosphatidylinositol-4,5-bisphosphate binding

Inferred from direct assay PubMed 22447935. Source: RGD

phosphatidylserine binding

Inferred from direct assay PubMed 18508778. Source: RGD

phospholipid binding

Inferred from direct assay Ref.1. Source: RGD

protein C-terminus binding

Inferred from physical interaction PubMed 19132534. Source: RGD

syntaxin binding

Inferred from direct assay PubMed 7791877. Source: BHF-UCL

syntaxin-1 binding

Inferred from direct assay PubMed 22711810. Source: RGD

transporter activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 421421Synaptotagmin-1
PRO_0000183940

Regions

Topological domain1 – 5757Vesicular Potential
Transmembrane58 – 7922Helical; Potential
Topological domain80 – 421342Cytoplasmic Potential
Domain143 – 244102C2 1
Domain274 – 377104C2 2
Region135 – 381247Phospholipid binding Probable
Compositional bias80 – 11940Lys-rich

Sites

Metal binding1711Calcium 2; via carbonyl oxygen
Metal binding1721Calcium 1
Metal binding1721Calcium 2
Metal binding1781Calcium 1
Metal binding2301Calcium 1
Metal binding2301Calcium 2
Metal binding2311Calcium 1; via carbonyl oxygen
Metal binding2321Calcium 1
Metal binding2321Calcium 2
Metal binding2321Calcium 3
Metal binding2351Calcium 3
Metal binding2361Calcium 3; via carbonyl oxygen
Metal binding2381Calcium 2
Metal binding2381Calcium 3

Amino acid modifications

Modified residue1281Phosphothreonine By similarity
Modified residue2291Phosphotyrosine By similarity
Lipidation741S-palmitoyl cysteine Ref.7
Lipidation751S-palmitoyl cysteine Ref.7
Lipidation771S-palmitoyl cysteine Ref.7
Lipidation791S-palmitoyl cysteine Ref.7
Lipidation821S-palmitoyl cysteine Ref.7
Glycosylation241N-linked (GlcNAc...)

Experimental info

Sequence conflict1881D → E in CAA36981. Ref.1
Sequence conflict3741G → D in CAA36981. Ref.1
Sequence conflict3931M → I in CAA36981. Ref.1

Secondary structure

............................................. 421
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P21707 [UniParc].

Last modified May 2, 2006. Version 3.
Checksum: 06CE28F04C97A722

FASTA42147,399
        10         20         30         40         50         60 
MVSASHPEAL AAPVTTVATL VPHNATEPAS PGEGKEDAFS KLKQKFMNEL HKIPLPPWAL 

        70         80         90        100        110        120 
IAIAIVAVLL VVTCCFCVCK KCLFKKKNKK KGKEKGGKNA INMKDVKDLG KTMKDQALKD 

       130        140        150        160        170        180 
DDAETGLTDG EEKEEPKEEE KLGKLQYSLD YDFQNNQLLV GIIQAAELPA LDMGGTSDPY 

       190        200        210        220        230        240 
VKVFLLPDKK KKFETKVHRK TLNPVFNEQF TFKVPYSELG GKTLVMAVYD FDRFSKHDII 

       250        260        270        280        290        300 
GEFKVPMNTV DFGHVTEEWR DLQSAEKEEQ EKLGDICFSL RYVPTAGKLT VVILEAKNLK 

       310        320        330        340        350        360 
KMDVGGLSDP YVKIHLMQNG KRLKKKKTTI KKNTLNPYYN ESFSFEVPFE QIQKVQVVVT 

       370        380        390        400        410        420 
VLDYDKIGKN DAIGKVFVGY NSTGAELRHW SDMLANPRRP IAQWHTLQVE EEVDAMLAVK 


K 

« Hide

References

[1]"Phospholipid binding by a synaptic vesicle protein homologous to the regulatory region of protein kinase C."
Perin M.S., Fried V.A., Mignery G.A., Jahn R., Suedhof T.C.
Nature 345:260-263(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Synaptotagmin gene content of the sequenced genomes."
Craxton M.A.
BMC Genomics 5:43-43(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"Functional analysis of synaptotagmin."
Sunitha S.S., Thekkuveettil A.
Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: Wistar.
[4]Lubec G., Chen W.-Q.
Submitted (APR-2007) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 214-233; 289-297; 355-366 AND 376-388, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: Sprague-Dawley.
Tissue: Hippocampus.
[5]"Isoform-specific, calcium-regulated interaction of the synaptic vesicle proteins SV2 and synaptotagmin."
Schivell A.E., Batchelor R.H., Bajjalieh S.M.
J. Biol. Chem. 271:27770-27775(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SV2A, DOMAIN.
[6]"Direct interaction of the Rab3 effector RIM with Ca2+ channels, SNAP-25, and synaptotagmin."
Coppola T., Magnin-Luethi S., Perret-Menoud V., Gattesco S., Schiavo G., Regazzi R.
J. Biol. Chem. 276:32756-32762(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RIMS1.
Tissue: Brain.
[7]"Palmitoylation sites and processing of synaptotagmin I, the putative calcium sensor for neurosecretion."
Heindel U., Schmidt M.F., Veit M.
FEBS Lett. 544:57-62(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PALMITOYLATION AT CYS-74; CYS-75; CYS-77; CYS-79 AND CYS-82.
[8]"SV2A and SV2C contain a unique synaptotagmin-binding site."
Schivell A.E., Mochida S., Kensel-Hammes P., Custer K.L., Bajjalieh S.M.
Mol. Cell. Neurosci. 29:56-64(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SV2A; SV2B AND SV2C.
[9]"Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold."
Sutton R.B., Davletov B.A., Berghuis A.M., Suedhof T.C., Sprang S.R.
Cell 80:929-938(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 132-266.
[10]"Solution structures of the Ca2+-free and Ca2+-bound C2A domain of synaptotagmin I: does Ca2+ induce a conformational change?"
Shao X., Fernandez I., Suedhof T.C., Rizo J.
Biochemistry 37:16106-16115(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 140-267.
[11]"Three-dimensional structure of the synaptotagmin 1 C2B-domain: synaptotagmin 1 as a phospholipid binding machine."
Fernandez I., Arac D., Ubach J., Gerber S.H., Shin O., Gao Y., Anderson R.G., Suedhof T.C., Rizo J.
Neuron 32:1057-1069(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 270-421.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X52772 mRNA. Translation: CAA36981.1.
AJ617615 mRNA. Translation: CAE85101.1.
DQ181550 mRNA. Translation: ABA00482.1.
PIRS09595.
RefSeqNP_001028852.2. NM_001033680.2.
UniGeneRn.216272.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP21707.
SMRP21707. Positions 140-418.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid247745. 1 interaction.
DIPDIP-29064N.
IntActP21707. 16 interactions.
MINTMINT-4542559.

PTM databases

PhosphoSiteP21707.

Proteomic databases

PaxDbP21707.
PRIDEP21707.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000048880; ENSRNOP00000049624; ENSRNOG00000006426.
GeneID25716.
KEGGrno:25716.
UCSCRGD:3803. rat.

Organism-specific databases

CTD6857.
RGD3803. Syt1.

Phylogenomic databases

eggNOGCOG5038.
GeneTreeENSGT00620000087641.
HOGENOMHOG000232127.
HOVERGENHBG005010.
InParanoidP21707.
KOK15290.
OMAHDIIGEY.
OrthoDBEOG78PV8W.
PhylomeDBP21707.
TreeFamTF315600.

Gene expression databases

ArrayExpressP21707.
GenevestigatorP21707.

Family and domain databases

Gene3D2.60.40.150. 2 hits.
InterProIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR015428. Synaptotagmin1/2.
[Graphical view]
PANTHERPTHR10024:SF117. PTHR10024:SF117. 1 hit.
PfamPF00168. C2. 2 hits.
[Graphical view]
PRINTSPR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTSM00239. C2. 2 hits.
[Graphical view]
SUPFAMSSF49562. SSF49562. 2 hits.
PROSITEPS50004. C2. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP21707.
NextBio607797.
PROP21707.

Entry information

Entry nameSYT1_RAT
AccessionPrimary (citable) accession number: P21707
Secondary accession number(s): Q3S2E6, Q707P5
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: May 2, 2006
Last modified: April 16, 2014
This is version 146 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references