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Q9H2B2

- SYT4_HUMAN

UniProt

Q9H2B2 - SYT4_HUMAN

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Protein

Synaptotagmin-4

Gene

SYT4

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

May be involved in Ca2+-dependent exocytosis of secretory vesicles through Ca2+ and phospholipid binding to the C2 domain or may serve as Ca2+ sensors in the process of vesicular trafficking and exocytosis.

Cofactori

Binds 3 calcium ions per subunit. The ions are bound to the C2 domains (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi184 – 1841Calcium 1By similarity
Metal bindingi184 – 1841Calcium 2By similarity
Metal bindingi191 – 1911Calcium 1By similarity
Metal bindingi245 – 2451Calcium 1; via carbonyl oxygenBy similarity
Metal bindingi246 – 2461Calcium 1By similarity
Metal bindingi246 – 2461Calcium 2By similarity
Metal bindingi246 – 2461Calcium 3By similarity
Metal bindingi249 – 2491Calcium 3By similarity
Metal bindingi252 – 2521Calcium 2By similarity
Metal bindingi252 – 2521Calcium 3By similarity

GO - Molecular functioni

  1. calcium ion binding Source: Ensembl
  2. phosphatidylserine binding Source: Ensembl
  3. transporter activity Source: InterPro

GO - Biological processi

  1. exocytosis Source: InterPro
  2. negative regulation of calcium ion-dependent exocytosis Source: Ensembl
  3. negative regulation of vesicle fusion Source: Ensembl
  4. neurotransmitter secretion Source: Ensembl
Complete GO annotation...

Keywords - Ligandi

Calcium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptotagmin-4
Alternative name(s):
Synaptotagmin IV
Short name:
SytIV
Gene namesi
Name:SYT4
Synonyms:KIAA1342
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 18

Organism-specific databases

HGNCiHGNC:11512. SYT4.

Subcellular locationi

GO - Cellular componenti

  1. cell junction Source: UniProtKB-KW
  2. dense core granule Source: Ensembl
  3. integral component of membrane Source: UniProtKB-KW
  4. neuron projection Source: Ensembl
  5. perinuclear region of cytoplasm Source: Ensembl
  6. synaptic vesicle Source: InterPro
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasmic vesicle, Membrane, Synapse

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA36293.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 425425Synaptotagmin-4PRO_0000183948Add
BLAST

Proteomic databases

PaxDbiQ9H2B2.
PRIDEiQ9H2B2.

PTM databases

PhosphoSiteiQ9H2B2.

Expressioni

Tissue specificityi

Expressed in brain. Within brain, expression is highest in hippocampus, with substantial levels also detected in amygdala and thalamus.

Gene expression databases

BgeeiQ9H2B2.
CleanExiHS_SYT4.
ExpressionAtlasiQ9H2B2. baseline and differential.
GenevestigatoriQ9H2B2.

Organism-specific databases

HPAiHPA010574.

Interactioni

Protein-protein interaction databases

BioGridi112724. 2 interactions.
IntActiQ9H2B2. 1 interaction.
MINTiMINT-1451266.
STRINGi9606.ENSP00000255224.

Structurei

Secondary structure

1
425
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi156 – 1649
Helixi165 – 1673
Beta strandi169 – 17911
Turni185 – 1884
Beta strandi191 – 1999
Turni200 – 2023
Beta strandi204 – 2074
Beta strandi218 – 2269
Helixi233 – 2353
Beta strandi237 – 2459
Beta strandi255 – 2606
Beta strandi271 – 2766

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UGKNMR-A154-278[»]
ProteinModelPortaliQ9H2B2.
SMRiQ9H2B2. Positions 152-425.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H2B2.

Topological domain

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 1616VesicularSequence AnalysisAdd
BLAST
Topological domaini38 – 425388CytoplasmicSequence AnalysisAdd
BLAST

Transmembrane

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei17 – 3721HelicalSequence AnalysisAdd
BLAST

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini155 – 258104C2 1PROSITE-ProRule annotationAdd
BLAST
Domaini289 – 392104C2 2PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni147 – 297151Phospholipid bindingCuratedAdd
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG292488.
GeneTreeiENSGT00760000118973.
HOGENOMiHOG000232126.
HOVERGENiHBG005010.
InParanoidiQ9H2B2.
OMAiQIAKWHM.
OrthoDBiEOG75J0N2.
PhylomeDBiQ9H2B2.
TreeFamiTF315600.

Family and domain databases

Gene3Di2.60.40.150. 2 hits.
InterProiIPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR028683. SYT4.
[Graphical view]
PANTHERiPTHR10024:SF114. PTHR10024:SF114. 1 hit.
PfamiPF00168. C2. 2 hits.
[Graphical view]
PRINTSiPR00399. SYNAPTOTAGMN.
SMARTiSM00239. C2. 2 hits.
[Graphical view]
SUPFAMiSSF49562. SSF49562. 2 hits.
PROSITEiPS50004. C2. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9H2B2-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAPITTSREE FDEIPTVVGI FSAFGLVFTV SLFAWICCQR KSSKSNKTPP
60 70 80 90 100
YKFVHVLKGV DIYPENLNSK KKFGADDKNE VKNKPAVPKN SLHLDLEKRD
110 120 130 140 150
LNGNFPKTNL KPGSPSDLEN ATPKLFLEGE KESVSPESLK SSTSLTSEEK
160 170 180 190 200
QEKLGTLFFS LEYNFERKAF VVNIKEARGL PAMDEQSMTS DPYIKMTILP
210 220 230 240 250
EKKHKVKTRV LRKTLDPAFD ETFTFYGIPY TQIQELALHF TILSFDRFSR
260 270 280 290 300
DDIIGEVLIP LSGIELSEGK MLMNREIIKR NVRKSSGRGE LLISLCYQST
310 320 330 340 350
TNTLTVVVLK ARHLPKSDVS GLSDPYVKVN LYHAKKRISK KKTHVKKCTP
360 370 380 390 400
NAVFNELFVF DIPCEGLEDI SVEFLVLDSE RGSRNEVIGQ LVLGAAAEGT
410 420
GGEHWKEICD YPRRQIAKWH VLCDG
Length:425
Mass (Da):47,958
Last modified:March 1, 2001 - v1
Checksum:iDA3D4CB175CB528D
GO
Isoform 2 (identifier: Q9H2B2-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     12-29: Missing.

Note: No experimental confirmation available.

Show »
Length:407
Mass (Da):46,064
Checksum:iCE234AC75CBDEB5C
GO

Sequence cautioni

The sequence BAA92580.1 differs from that shown. Reason: Erroneous initiation.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti142 – 1421S → N.
Corresponds to variant rs16977447 [ dbSNP | Ensembl ].
VAR_052239

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei12 – 2918Missing in isoform 2. 1 PublicationVSP_056643Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF299075 mRNA. Translation: AAG37229.1.
AB037763 mRNA. Translation: BAA92580.1. Different initiation.
AK293791 mRNA. Translation: BAG57204.1.
AC091039 Genomic DNA. No translation available.
BC036538 mRNA. Translation: AAH36538.1.
CCDSiCCDS11922.1. [Q9H2B2-1]
RefSeqiNP_065834.1. NM_020783.3.
UniGeneiHs.8059.

Genome annotation databases

EnsembliENST00000255224; ENSP00000255224; ENSG00000132872. [Q9H2B2-1]
ENST00000590752; ENSP00000466930; ENSG00000132872. [Q9H2B2-2]
GeneIDi6860.
KEGGihsa:6860.
UCSCiuc002law.3. human. [Q9H2B2-1]

Polymorphism databases

DMDMi18202937.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF299075 mRNA. Translation: AAG37229.1 .
AB037763 mRNA. Translation: BAA92580.1 . Different initiation.
AK293791 mRNA. Translation: BAG57204.1 .
AC091039 Genomic DNA. No translation available.
BC036538 mRNA. Translation: AAH36538.1 .
CCDSi CCDS11922.1. [Q9H2B2-1 ]
RefSeqi NP_065834.1. NM_020783.3.
UniGenei Hs.8059.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1UGK NMR - A 154-278 [» ]
ProteinModelPortali Q9H2B2.
SMRi Q9H2B2. Positions 152-425.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 112724. 2 interactions.
IntActi Q9H2B2. 1 interaction.
MINTi MINT-1451266.
STRINGi 9606.ENSP00000255224.

PTM databases

PhosphoSitei Q9H2B2.

Polymorphism databases

DMDMi 18202937.

Proteomic databases

PaxDbi Q9H2B2.
PRIDEi Q9H2B2.

Protocols and materials databases

DNASUi 6860.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000255224 ; ENSP00000255224 ; ENSG00000132872 . [Q9H2B2-1 ]
ENST00000590752 ; ENSP00000466930 ; ENSG00000132872 . [Q9H2B2-2 ]
GeneIDi 6860.
KEGGi hsa:6860.
UCSCi uc002law.3. human. [Q9H2B2-1 ]

Organism-specific databases

CTDi 6860.
GeneCardsi GC18M040847.
HGNCi HGNC:11512. SYT4.
HPAi HPA010574.
MIMi 600103. gene.
neXtProti NX_Q9H2B2.
PharmGKBi PA36293.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG292488.
GeneTreei ENSGT00760000118973.
HOGENOMi HOG000232126.
HOVERGENi HBG005010.
InParanoidi Q9H2B2.
OMAi QIAKWHM.
OrthoDBi EOG75J0N2.
PhylomeDBi Q9H2B2.
TreeFami TF315600.

Miscellaneous databases

EvolutionaryTracei Q9H2B2.
GeneWikii SYT4.
GenomeRNAii 6860.
NextBioi 26771.
PROi Q9H2B2.
SOURCEi Search...

Gene expression databases

Bgeei Q9H2B2.
CleanExi HS_SYT4.
ExpressionAtlasi Q9H2B2. baseline and differential.
Genevestigatori Q9H2B2.

Family and domain databases

Gene3Di 2.60.40.150. 2 hits.
InterProi IPR000008. C2_dom.
IPR001565. Synaptotagmin.
IPR028683. SYT4.
[Graphical view ]
PANTHERi PTHR10024:SF114. PTHR10024:SF114. 1 hit.
Pfami PF00168. C2. 2 hits.
[Graphical view ]
PRINTSi PR00399. SYNAPTOTAGMN.
SMARTi SM00239. C2. 2 hits.
[Graphical view ]
SUPFAMi SSF49562. SSF49562. 2 hits.
PROSITEi PS50004. C2. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The human synaptotagmin IV gene defines an evolutionary break point between syntenic mouse and human chromosome regions but retains ligand inducibility and tissue specificity."
    Ferguson G.D., Chen X.-N., Korenberg J.R., Herschman H.R.
    J. Biol. Chem. 275:36920-36926(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.
    DNA Res. 7:65-73(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Cerebellum.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  6. "Solution structure of the first C2 domain of synaptotagmin IV from human fetal brain (KIAA1342)."
    RIKEN structural genomics initiative (RSGI)
    Submitted (DEC-2003) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 154-278.

Entry informationi

Entry nameiSYT4_HUMAN
AccessioniPrimary (citable) accession number: Q9H2B2
Secondary accession number(s): B4DEU3, Q9P2K4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: March 1, 2001
Last modified: October 29, 2014
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 18
    Human chromosome 18: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3