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P21707

- SYT1_RAT

UniProt

P21707 - SYT1_RAT

Protein

Synaptotagmin-1

Gene

Syt1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 150 (01 Oct 2014)
      Sequence version 3 (02 May 2006)
      Previous versions | rss
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    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

    Binds 3 calcium 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 binding Source: UniProtKB
    11. protein C-terminus binding Source: RGD
    12. SNARE binding Source: RGD
    13. syntaxin-1 binding Source: RGD
    14. syntaxin binding Source: BHF-UCL
    15. transporter activity Source: InterPro

    GO - Biological processi

    1. calcium ion-dependent exocytosis Source: RGD
    2. detection of calcium ion Source: RGD
    3. positive regulation of calcium ion-dependent exocytosis Source: RGD
    4. positive regulation of vesicle fusion Source: RGD
    5. regulation of calcium ion-dependent exocytosis Source: RGD
    6. response to calcium ion Source: RGD
    7. synaptic vesicle exocytosis Source: RGD
    8. vesicle docking Source: RGD

    Keywords - Ligandi

    Calcium, Metal-binding

    Enzyme and pathway databases

    ReactomeiREACT_227883. Glutamate Neurotransmitter Release Cycle.

    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

    GO - Cellular componenti

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

    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

    ArrayExpressiP21707.
    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 – 1529
    Turni153 – 1564
    Beta strandi157 – 16711
    Beta strandi179 – 1868
    Beta strandi205 – 2128
    Helixi216 – 2194
    Beta strandi223 – 2308
    Beta strandi233 – 2353
    Beta strandi238 – 2469
    Helixi247 – 2493
    Beta strandi256 – 2616
    Beta strandi275 – 2839
    Turni284 – 2874
    Beta strandi288 – 29811
    Beta strandi310 – 3189
    Beta strandi321 – 3277
    Beta strandi338 – 3469
    Helixi349 – 3546
    Beta strandi356 – 3638
    Beta strandi366 – 3683
    Beta strandi371 – 3799
    Helixi384 – 39512
    Beta strandi396 – 3994
    Beta strandi401 – 4066
    Helixi410 – 4178

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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[»]
    ProteinModelPortaliP21707.
    SMRiP21707. Positions 140-418.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21707.

    Topological domain

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

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei58 – 7922HelicalSequence AnalysisAdd
    BLAST

    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.
    GeneTreeiENSGT00620000087641.
    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

    MVSASHPEAL AAPVTTVATL VPHNATEPAS PGEGKEDAFS KLKQKFMNEL    50
    HKIPLPPWAL IAIAIVAVLL VVTCCFCVCK KCLFKKKNKK KGKEKGGKNA 100
    INMKDVKDLG KTMKDQALKD DDAETGLTDG EEKEEPKEEE KLGKLQYSLD 150
    YDFQNNQLLV GIIQAAELPA LDMGGTSDPY VKVFLLPDKK KKFETKVHRK 200
    TLNPVFNEQF TFKVPYSELG GKTLVMAVYD FDRFSKHDII GEFKVPMNTV 250
    DFGHVTEEWR DLQSAEKEEQ EKLGDICFSL RYVPTAGKLT VVILEAKNLK 300
    KMDVGGLSDP YVKIHLMQNG KRLKKKKTTI KKNTLNPYYN ESFSFEVPFE 350
    QIQKVQVVVT VLDYDKIGKN DAIGKVFVGY NSTGAELRHW SDMLANPRRP 400
    IAQWHTLQVE EEVDAMLAVK K 421
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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:
    PDBe
    RCSB PDB
    PDBj
    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 [» ]
    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 ENSGT00620000087641.
    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.

    Miscellaneous databases

    EvolutionaryTracei P21707.
    NextBioi 607797.
    PROi P21707.

    Gene expression databases

    ArrayExpressi P21707.
    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: October 1, 2014
    This is version 150 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