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P21707

- SYT1_RAT

UniProt

P21707 - SYT1_RAT

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Protein

Synaptotagmin-1

Gene

Syt1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - 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.

Cofactori

Ca2+Note: Binds 3 Ca(2+) ions per subunit. The ions are bound to the C2 domains.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi171 – 1711Calcium 2; via carbonyl oxygen
Metal bindingi172 – 1721Calcium 1
Metal bindingi172 – 1721Calcium 2
Metal bindingi178 – 1781Calcium 1
Metal bindingi230 – 2301Calcium 1
Metal bindingi230 – 2301Calcium 2
Metal bindingi231 – 2311Calcium 1; via carbonyl oxygen
Metal bindingi232 – 2321Calcium 1
Metal bindingi232 – 2321Calcium 2
Metal bindingi232 – 2321Calcium 3
Metal bindingi235 – 2351Calcium 3
Metal bindingi236 – 2361Calcium 3; via carbonyl oxygen
Metal bindingi238 – 2381Calcium 2
Metal bindingi238 – 2381Calcium 3

GO - Molecular functioni

  1. calcium-dependent phospholipid binding Source: BHF-UCL
  2. calcium-dependent protein binding Source: RGD
  3. calcium ion binding Source: RGD
  4. calmodulin binding Source: RGD
  5. clathrin binding Source: BHF-UCL
  6. identical protein binding Source: IntAct
  7. phosphatidylinositol-4,5-bisphosphate binding Source: RGD
  8. phosphatidylserine binding Source: RGD
  9. phospholipid binding Source: RGD
  10. protein C-terminus binding Source: RGD
  11. SNARE binding Source: ParkinsonsUK-UCL
  12. syntaxin-1 binding Source: ParkinsonsUK-UCL
  13. syntaxin binding Source: BHF-UCL
  14. transporter activity Source: InterPro

GO - Biological processi

  1. calcium ion-dependent exocytosis Source: RGD
  2. calcium ion-dependent exocytosis of neurotransmitter Source: ParkinsonsUK-UCL
  3. detection of calcium ion Source: RGD
  4. positive regulation of calcium ion-dependent exocytosis Source: RGD
  5. positive regulation of synaptic transmission Source: ParkinsonsUK-UCL
  6. positive regulation of vesicle fusion Source: RGD
  7. regulation of calcium ion-dependent exocytosis Source: RGD
  8. regulation of regulated secretory pathway Source: ParkinsonsUK-UCL
  9. regulation of synaptic transmission, glutamatergic Source: ParkinsonsUK-UCL
  10. response to calcium ion Source: RGD
  11. synaptic vesicle exocytosis Source: RGD
  12. vesicle docking Source: RGD
Complete GO annotation...

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

ReactomeiREACT_227883. Glutamate Neurotransmitter Release Cycle.
REACT_245524. Acetylcholine Neurotransmitter Release Cycle.
REACT_246747. Norepinephrine Neurotransmitter Release Cycle.
REACT_262380. 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
ProteomesiUP000002494: Chromosome 7

Organism-specific databases

RGDi3803. Syt1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 5757VesicularSequence AnalysisAdd
BLAST
Transmembranei58 – 7922HelicalSequence AnalysisAdd
BLAST
Topological domaini80 – 421342CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. cell junction Source: UniProtKB-KW
  2. cytoplasm Source: MGI
  3. dense core granule Source: MGI
  4. excitatory synapse Source: BHF-UCL
  5. integral component of membrane Source: UniProtKB-KW
  6. intracellular organelle Source: RGD
  7. neuron projection Source: Ensembl
  8. plasma membrane Source: BHF-UCL
  9. presynaptic membrane Source: Ensembl
  10. secretory granule Source: RGD
  11. synaptic vesicle Source: BHF-UCL
  12. synaptic vesicle membrane Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasm, Cytoplasmic vesicle, Membrane, Synapse

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 421421Synaptotagmin-1PRO_0000183940Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi24 – 241N-linked (GlcNAc...)
Lipidationi74 – 741S-palmitoyl cysteine1 Publication
Lipidationi75 – 751S-palmitoyl cysteine1 Publication
Lipidationi77 – 771S-palmitoyl cysteine1 Publication
Lipidationi79 – 791S-palmitoyl cysteine1 Publication
Lipidationi82 – 821S-palmitoyl cysteine1 Publication
Modified residuei128 – 1281PhosphothreonineBy similarity
Modified residuei229 – 2291PhosphotyrosineBy similarity

Keywords - PTMi

Glycoprotein, Lipoprotein, Palmitate, Phosphoprotein

Proteomic databases

PaxDbiP21707.
PRIDEiP21707.

PTM databases

PhosphoSiteiP21707.

Expressioni

Tissue specificityi

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

Gene expression databases

ExpressionAtlasiP21707. baseline and differential.
GenevestigatoriP21707.

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 similarity3 PublicationsCurated

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

Protein-protein interaction databases

BioGridi247745. 1 interaction.
DIPiDIP-29064N.
IntActiP21707. 16 interactions.
MINTiMINT-4542559.

Structurei

Secondary structure

1
421
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi144 – 1529Combined sources
Turni153 – 1564Combined sources
Beta strandi157 – 16711Combined sources
Beta strandi179 – 1868Combined sources
Beta strandi205 – 2128Combined sources
Helixi216 – 2194Combined sources
Beta strandi223 – 2308Combined sources
Beta strandi233 – 2353Combined sources
Beta strandi238 – 2469Combined sources
Helixi247 – 2493Combined sources
Beta strandi256 – 2616Combined sources
Beta strandi275 – 2839Combined sources
Turni284 – 2874Combined sources
Beta strandi288 – 29811Combined sources
Beta strandi310 – 3189Combined sources
Beta strandi321 – 3277Combined sources
Beta strandi338 – 3469Combined sources
Helixi349 – 3546Combined sources
Beta strandi356 – 3638Combined sources
Beta strandi366 – 3683Combined sources
Beta strandi371 – 3799Combined sources
Helixi384 – 39512Combined sources
Beta strandi396 – 3994Combined sources
Beta strandi401 – 4066Combined sources
Helixi410 – 4178Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP21707.
SMRiP21707. Positions 140-418.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21707.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini143 – 244102C2 1PROSITE-ProRule annotationAdd
BLAST
Domaini274 – 377104C2 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni135 – 381247Phospholipid bindingCuratedAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi80 – 11940Lys-richAdd
BLAST

Domaini

The first C2 domain mediates Ca2+-dependent phospholipid binding.1 Publication
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

eggNOGiCOG5038.
GeneTreeiENSGT00760000118973.
HOGENOMiHOG000232127.
HOVERGENiHBG005010.
InParanoidiP21707.
KOiK15290.
OMAiHDIIGEY.
OrthoDBiEOG78PV8W.
PhylomeDBiP21707.
TreeFamiTF315600.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR015428. Synaptotagmin1.
[Graphical view]
PANTHERiPTHR10024:SF183. PTHR10024:SF183. 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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti188 – 1881D → E in CAA36981. (PubMed:2333096)Curated
Sequence conflicti374 – 3741G → D in CAA36981. (PubMed:2333096)Curated
Sequence conflicti393 – 3931M → I in CAA36981. (PubMed:2333096)Curated

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.
UniGeneiRn.216272.

Genome annotation databases

EnsembliENSRNOT00000048880; ENSRNOP00000049624; 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 .
PIRi S09595.
RefSeqi NP_001028852.2. NM_001033680.2.
UniGenei Rn.216272.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1BYN NMR - A 140-267 [» ]
1K5W NMR - A 270-421 [» ]
1RSY X-ray 1.90 A 132-266 [» ]
1TJM X-ray 1.18 A 271-421 [» ]
1TJX X-ray 1.04 A 271-421 [» ]
1UOV X-ray 1.65 A 271-421 [» ]
1UOW X-ray 1.04 A 271-421 [» ]
2YOA X-ray 1.50 A/B 271-421 [» ]
4WEE X-ray 0.89 A 140-266 [» ]
ProteinModelPortali P21707.
SMRi P21707. Positions 140-418.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 247745. 1 interaction.
DIPi DIP-29064N.
IntActi P21707. 16 interactions.
MINTi MINT-4542559.

PTM databases

PhosphoSitei P21707.

Proteomic databases

PaxDbi P21707.
PRIDEi P21707.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000048880 ; ENSRNOP00000049624 ; ENSRNOG00000006426 .
GeneIDi 25716.
KEGGi rno:25716.
UCSCi RGD:3803. rat.

Organism-specific databases

CTDi 6857.
RGDi 3803. Syt1.

Phylogenomic databases

eggNOGi COG5038.
GeneTreei ENSGT00760000118973.
HOGENOMi HOG000232127.
HOVERGENi HBG005010.
InParanoidi P21707.
KOi K15290.
OMAi HDIIGEY.
OrthoDBi EOG78PV8W.
PhylomeDBi P21707.
TreeFami TF315600.

Enzyme and pathway databases

Reactomei REACT_227883. Glutamate Neurotransmitter Release Cycle.
REACT_245524. Acetylcholine Neurotransmitter Release Cycle.
REACT_246747. Norepinephrine Neurotransmitter Release Cycle.
REACT_262380. GABA synthesis, release, reuptake and degradation.

Miscellaneous databases

EvolutionaryTracei P21707.
NextBioi 607797.
PROi P21707.

Gene expression databases

ExpressionAtlasi P21707. baseline and differential.
Genevestigatori P21707.

Family and domain databases

Gene3Di 2.60.40.150. 2 hits.
InterProi IPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR015428. Synaptotagmin1.
[Graphical view ]
PANTHERi PTHR10024:SF183. PTHR10024:SF183. 1 hit.
Pfami PF00168. C2. 2 hits.
[Graphical view ]
PRINTSi PR00360. C2DOMAIN.
PR00399. SYNAPTOTAGMN.
SMARTi SM00239. C2. 2 hits.
[Graphical view ]
SUPFAMi SSF49562. SSF49562. 2 hits.
PROSITEi PS50004. C2. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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. 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.

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 26, 2014
This is version 152 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

External Data

Dasty 3