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Protein

Synaptotagmin-3

Gene

Syt3

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

Functioni

Ca2+ sensor involved in Ca2+-dependent exocytosis of secretory vesicles through Ca2+ and phospholipid binding to the C2 domain. Ca2+ induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (PubMed:11823420, PubMed:18508778). Plays a role in dendrite formation by melanocytes (By similarity).By similarity2 Publications

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 bindingi328Calcium 1Combined sources1 Publication1
Metal bindingi328Calcium 2Combined sources1 Publication1
Metal bindingi334Calcium 1Combined sources1 Publication1
Metal bindingi386Calcium 1Combined sources1 Publication1
Metal bindingi386Calcium 2Combined sources1 Publication1
Metal bindingi387Calcium 1; via carbonyl oxygenCombined sources1 Publication1
Metal bindingi388Calcium 1Combined sources1 Publication1
Metal bindingi388Calcium 2Combined sources1 Publication1
Metal bindingi388Calcium 3Combined sources1 Publication1
Metal bindingi391Calcium 3Combined sources1 Publication1
Metal bindingi394Calcium 2Combined sources1 Publication1
Metal bindingi394Calcium 3Combined sources1 Publication1

GO - Molecular functioni

  • calcium-dependent phospholipid binding Source: RGD
  • calcium ion binding Source: RGD
  • clathrin binding Source: BHF-UCL
  • phosphatidylinositol-4,5-bisphosphate binding Source: ParkinsonsUK-UCL
  • phosphatidylserine binding Source: ParkinsonsUK-UCL
  • SNARE binding Source: ParkinsonsUK-UCL
  • syntaxin binding Source: RGD

GO - Biological processi

  • calcium ion regulated exocytosis Source: RGD
  • calcium ion-regulated exocytosis of neurotransmitter Source: GO_Central
  • cell differentiation Source: UniProtKB-KW
  • positive regulation of vesicle fusion Source: RGD
  • regulation of calcium ion-dependent exocytosis Source: ParkinsonsUK-UCL
  • response to calcium ion Source: RGD
  • synaptic vesicle exocytosis Source: RGD
Complete GO annotation...

Keywords - Biological processi

Differentiation

Keywords - Ligandi

Calcium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptotagmin-3
Alternative name(s):
Synaptotagmin III
Short name:
SytIII
Gene namesi
Name:Syt3
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi3805. Syt3.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 54VesicularSequence analysisAdd BLAST54
Transmembranei55 – 75HelicalSequence analysisAdd BLAST21
Topological domaini76 – 588CytoplasmicSequence analysisAdd BLAST513

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi334D → N: Abolishes Ca(2+)-dependent phospholipid-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001839471 – 588Synaptotagmin-3Add BLAST588

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei286Omega-N-methylarginineBy similarity1

Keywords - PTMi

Disulfide bond, Methylation

Proteomic databases

PaxDbiP40748.
PRIDEiP40748.

PTM databases

iPTMnetiP40748.
PhosphoSitePlusiP40748.

Expressioni

Tissue specificityi

Brain, various endocrine tissues and hormone-secreting clonal cells.1 Publication

Gene expression databases

BgeeiENSRNOG00000019318.

Interactioni

Subunit structurei

Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT6, SYT9 and SYT10.By similarity

GO - Molecular functioni

  • clathrin binding Source: BHF-UCL
  • SNARE binding Source: ParkinsonsUK-UCL
  • syntaxin binding Source: RGD

Protein-protein interaction databases

BioGridi247760. 1 interactor.
IntActiP40748. 2 interactors.
STRINGi10116.ENSRNOP00000026251.

Structurei

Secondary structure

1588
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi300 – 306Combined sources7
Beta strandi309 – 311Combined sources3
Beta strandi313 – 322Combined sources10
Beta strandi335 – 340Combined sources6
Beta strandi344 – 350Combined sources7
Beta strandi361 – 369Combined sources9
Helixi372 – 375Combined sources4
Beta strandi381 – 386Combined sources6
Beta strandi389 – 391Combined sources3
Beta strandi395 – 400Combined sources6
Helixi406 – 408Combined sources3
Beta strandi412 – 414Combined sources3
Beta strandi416 – 419Combined sources4
Beta strandi432 – 440Combined sources9
Turni441 – 444Combined sources4
Beta strandi445 – 455Combined sources11
Beta strandi460 – 463Combined sources4
Beta strandi467 – 471Combined sources5
Beta strandi478 – 484Combined sources7
Beta strandi490 – 493Combined sources4
Beta strandi495 – 498Combined sources4
Beta strandi501 – 503Combined sources3
Helixi507 – 510Combined sources4
Beta strandi517 – 520Combined sources4
Beta strandi523 – 525Combined sources3
Beta strandi528 – 532Combined sources5
Helixi542 – 549Combined sources8
Beta strandi551 – 557Combined sources7
Beta strandi561 – 564Combined sources4
Helixi568 – 570Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DQVX-ray3.20A293-588[»]
3HN8X-ray3.50A/B/C292-587[»]
ProteinModelPortaliP40748.
SMRiP40748.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP40748.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini299 – 400C2 1PROSITE-ProRule annotationAdd BLAST102
Domaini431 – 534C2 2PROSITE-ProRule annotationAdd BLAST104

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni10 – 34Cysteine motifBy similarityAdd BLAST25

Domaini

The first C2 domain mediates Ca2+-dependent phospholipid binding.1 Publication
The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.By similarity

Sequence similaritiesi

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

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410KDMB. Eukaryota.
COG5038. LUCA.
HOGENOMiHOG000232128.
HOVERGENiHBG005010.
InParanoidiP40748.
KOiK19903.
PhylomeDBiP40748.
TreeFamiTF315600.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR028682. SYT3.
[Graphical view]
PANTHERiPTHR10024:SF176. PTHR10024:SF176. 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.

P40748-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGDYEDDLC RRALILVSDL CARIRDADTN DRCQEFNELR IRGYPRGPDA
60 70 80 90 100
DISVSLLSVI VTFCGIVLLG VSLFVSWKLC WVPWRDKGGS AVGGGPLRKD
110 120 130 140 150
LAPGVGLAGL VGGGGHHLGA SLGGHPLLGG PHHHAHPAHH PPFAELLEPG
160 170 180 190 200
GLGGSEPPEP SYLDMDSYPE AAVASVVAAG VKPSQTSPEL PSEGGTGSGL
210 220 230 240 250
LLLPPSGGGL PSAQSHQQVT SLAPTTRYPA LPRPLTQQTL TTQADPSSEE
260 270 280 290 300
RPPALPLPLP GGEEKAKLIG QIKPELYQGT GPGGRRTGGG SGEAGAPCGR
310 320 330 340 350
ISFALRYLYG SDQLVVRILQ ALDLPAKDSN GFSDPYVKIY LLPDRKKKFQ
360 370 380 390 400
TKVHRKTLNP IFNETFQFSV PLAELAQRKL HFSVYDFDRF SRHDLIGQVV
410 420 430 440 450
LDNLLELAEQ PPDRPLWRDI LEGGSEKADL GELNFSLCYL PTAGLLTVTI
460 470 480 490 500
IKASNLKAMD LTGFSDPYVK ASLISEGRRL KKRKTSIKKN TLNPTYNEAL
510 520 530 540 550
VFDVAPESVE NVGLSIAVVD YDCIGHNEVI GVCRVGPEAA DPHGREHWAE
560 570 580
MLANPRKPVE HWHQLVEEKT LSSFTKGGKG LSEKENSE
Length:588
Mass (Da):63,313
Last modified:February 1, 1995 - v1
Checksum:i9D9D33CF5BAD8331
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti287T → S in AAK56959 (Ref. 2) Curated1
Sequence conflicti445L → R in AAK56959 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D28512 mRNA. Translation: BAA05870.1.
AF375464 mRNA. Translation: AAK56959.1.
PIRiA53563.
RefSeqiNP_061995.1. NM_019122.1.
XP_006229040.1. XM_006228978.3.
XP_006229041.1. XM_006228979.3.
XP_008757547.1. XM_008759325.2.
XP_017444322.1. XM_017588833.1.
UniGeneiRn.48884.

Genome annotation databases

GeneIDi25731.
KEGGirno:25731.
UCSCiRGD:3805. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D28512 mRNA. Translation: BAA05870.1.
AF375464 mRNA. Translation: AAK56959.1.
PIRiA53563.
RefSeqiNP_061995.1. NM_019122.1.
XP_006229040.1. XM_006228978.3.
XP_006229041.1. XM_006228979.3.
XP_008757547.1. XM_008759325.2.
XP_017444322.1. XM_017588833.1.
UniGeneiRn.48884.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DQVX-ray3.20A293-588[»]
3HN8X-ray3.50A/B/C292-587[»]
ProteinModelPortaliP40748.
SMRiP40748.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi247760. 1 interactor.
IntActiP40748. 2 interactors.
STRINGi10116.ENSRNOP00000026251.

PTM databases

iPTMnetiP40748.
PhosphoSitePlusiP40748.

Proteomic databases

PaxDbiP40748.
PRIDEiP40748.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi25731.
KEGGirno:25731.
UCSCiRGD:3805. rat.

Organism-specific databases

CTDi84258.
RGDi3805. Syt3.

Phylogenomic databases

eggNOGiENOG410KDMB. Eukaryota.
COG5038. LUCA.
HOGENOMiHOG000232128.
HOVERGENiHBG005010.
InParanoidiP40748.
KOiK19903.
PhylomeDBiP40748.
TreeFamiTF315600.

Miscellaneous databases

EvolutionaryTraceiP40748.
PROiP40748.

Gene expression databases

BgeeiENSRNOG00000019318.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR028682. SYT3.
[Graphical view]
PANTHERiPTHR10024:SF176. PTHR10024:SF176. 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 nameiSYT3_RAT
AccessioniPrimary (citable) accession number: P40748
Secondary accession number(s): Q925B7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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.