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(-) Description

Title :  RAT SYNAPTOTAGMIN 4 C2B DOMAIN IN THE PRESENCE OF CALCIUM
 
Authors :  H. Dai, O. -H. Shin, M. Machius, D. R. Tomchick, T. C. Sudhof, J. Rizo
Date :  16 Jun 04  (Deposition) - 13 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Metal Binding Protein, Synaptotagmin, Endocytosis/Exocytosis, Neurotransmitter Release, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Dai, O. -H. Shin, M. Machius, D. R. Tomchick, T. C. Sudhof, J. Rizo
Structural Basis For The Evolutionary Inactivation Of Ca2+ Binding To Synaptotagmin 4
Nat. Struct. Mol. Biol. V. 11 844 2004
PubMed-ID: 15311271  |  Reference-DOI: 10.1038/NSMB817

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN IV
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentC2B DOMAIN, RESIDUES 288-425
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL9Ligand/IonCHLORIDE ION
3NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:324 , ASP A:378 , SER A:379 , GLU A:380 , HOH A:2049BINDING SITE FOR RESIDUE CA A1001
02AC2SOFTWAREGLU A:365 , ASP A:410 , HOH A:2010 , HOH A:2042 , HOH A:2071 , HOH A:2072 , HOH A:2076BINDING SITE FOR RESIDUE CA A1002
03AC3SOFTWAREGLU A:386 , ASP A:424 , GLY A:425 , HOH A:2062BINDING SITE FOR RESIDUE CA A1003
04AC4SOFTWARESER A:339 , ASP A:361BINDING SITE FOR RESIDUE NA A2001
05AC5SOFTWAREGLU A:380 , SER A:383 , ASN A:385 , HOH A:2050 , HOH A:2054 , HOH A:2059BINDING SITE FOR RESIDUE NA A2002
06AC6SOFTWAREASN A:355BINDING SITE FOR RESIDUE CL A3001
07AC7SOFTWAREVAL A:359 , TRP A:419 , HOH A:2086 , HOH A:2087BINDING SITE FOR RESIDUE CL A3002
08AC8SOFTWARETYR A:326 , LYS A:328 , ARG A:384 , HOH A:2018BINDING SITE FOR RESIDUE CL A3003
09AC9SOFTWARELYS A:341 , PHE A:358 , VAL A:359 , TRP A:419BINDING SITE FOR RESIDUE CL A3004
10BC1SOFTWARELYS A:328 , ASN A:330 , ARG A:384BINDING SITE FOR RESIDUE CL A3005
11BC2SOFTWARELYS A:328 , ARG A:337 , LYS A:340BINDING SITE FOR RESIDUE CL A3006
12BC3SOFTWAREARG A:312 , HIS A:313 , HOH A:2005BINDING SITE FOR RESIDUE CL A3007
13BC4SOFTWARELEU A:367 , HOH A:2073BINDING SITE FOR RESIDUE CL A3009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W15)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT4_RAT170-258
302-392
  1-
A:302-392
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT4_RAT170-258
302-392
  3-
A:302-392

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000235941ENSRNOE00000166960chr18:23814489-23814218272SYT4_RAT1-12120--
1.2ENSRNOT000000235942ENSRNOE00000166314chr18:23811409-23810595815SYT4_RAT12-2832720--
1.3ENSRNOT000000235943ENSRNOE00000166526chr18:23808854-23808734121SYT4_RAT284-324411A:288-324 (gaps)37
1.4ENSRNOT000000235944ENSRNOE00000165428chr18:23807748-238050802669SYT4_RAT324-4251021A:324-425102

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:132
 aligned with SYT4_RAT | P50232 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:138
                                   297       307       317       327       337       347       357       367       377       387       397       407       417        
             SYT4_RAT   288 RGELLVSLCYQSTTNTLTVVVLKARHLPKSDVSGLSDPYVKVNLYHAKKRISKKKTHVKKCTPNAVFNELFVFDIPCESLEEISVEFLVLDSERGSRNEVIGRLVLGATAEGSGGGHWKEICDFPRRQIAKWHMLCDG 425
               SCOP domains d1w15a_ A: Synaptotagmin IV                                                                                                                SCOP domains
               CATH domains 1w15A00 A:288-425 C2- domain       Calcium/lipid binding domain                                                                            CATH domains
               Pfam domains ----------------C2-1w15A01 A      :304-392                                                               --------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....eeeeeeeeee...------...eeeeeeeee..eeeeeee.........eeeeeeeeee........eeeeeeeee.......eeeeeeee.....hhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------C2  PDB: A:302-392 UniProt: 302-392                                                        --------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:288-324 (gaps)      ----------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.4  PDB: A:324-425 UniProt: 324-425                                                              Transcript 1 (2)
                 1w15 A 288 RGELLVSLCYQSTTNTLTVVVLKARHLP------LSDPYVKVNLYHAKKRISKKKTHVKKCTPNAVFNELFVFDIPCESLEEISVEFLVLDSERGSRNEVIGRLVLGATAEGSGGGHWKEICDFPRRQIAKWHMLCDG 425
                                   297       307       | -    |  327       337       347       357       367       377       387       397       407       417        
                                                     315    322                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: C2 (71)

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYT4_RAT | P50232)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005544    calcium-dependent phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
    GO:0030276    clathrin binding    Interacting selectively and non-covalently with a clathrin heavy or light chain, the main components of the coat of coated vesicles and coated pits, and which also occurs in synaptic vesicles.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019905    syntaxin binding    Interacting selectively and non-covalently with a syntaxin, a SNAP receptor involved in the docking of synaptic vesicles at the presynaptic zone of a synapse.
biological process
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0017156    calcium ion regulated exocytosis    The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.
    GO:0048791    calcium ion-regulated exocytosis of neurotransmitter    The release of a neurotransmitter into the synaptic cleft by exocytosis of synaptic vesicles, where the release step is dependent on a rise in cytosolic calcium ion levels.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0045955    negative regulation of calcium ion-dependent exocytosis    Any process that stops, prevents, or reduces the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:0031339    negative regulation of vesicle fusion    Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:1903861    positive regulation of dendrite extension    Any process that activates or increases the frequency, rate or extent of dendrite extension.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0031045    dense core granule    Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
    GO:0030672    synaptic vesicle membrane    The lipid bilayer surrounding a synaptic vesicle.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYT4_RAT | P502321w16

(-) Related Entries Specified in the PDB File

1w16 RAT SYNAPTOTAGMIN 4 C2B DOMAIN IN THE ABSENCE OF CALCIUM