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(-) Description

Title :  CALCIUM BINDING DOMAIN C2B
 
Authors :  Y. Cheng, S. M. Sequeira, T. H. Sollner, D. J. Patel
Date :  24 Sep 03  (Deposition) - 09 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Transmembrane, Synapse, Glycoprotein, Lipoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Cheng, S. M. Sequeira, L. Malinina, V. Tereshko, T. H. Sollner, D. J. Patel
Crystallographic Identification Of Ca2+ And Sr2+ Coordination Sites In Synaptotagmin I C2B Domain
Protein Sci. V. 13 2665 2004
PubMed-ID: 15340165  |  Reference-DOI: 10.1110/PS.04832604

(-) Compounds

Molecule 1 - SYNAPTOTAGMIN I
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: C2B DOMAIN, RESIDUES 271-421
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: 3 CALCIUM IONS BOUND
    Synonym: SYTI, P65

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:302 , ASP A:303 , ASP A:363 , ASP A:365 , HOH A:2021 , HOH A:2024 , HOH A:2084BINDING SITE FOR RESIDUE CA A1419
2AC2SOFTWAREASP A:303 , ASP A:309 , ASP A:363 , TYR A:364 , ASP A:365 , HOH A:2085BINDING SITE FOR RESIDUE CA A1420
3AC3SOFTWAREASP A:303 , ASP A:309 , ASN A:333 , HOH A:2023 , HOH A:2028 , HOH A:2029 , HOH A:2053BINDING SITE FOR RESIDUE CA A1421
4AC4SOFTWARETYR A:339 , ASN A:340 , THR A:383 , GLY A:384 , HOH A:2063 , HOH A:2064 , HOH A:2121 , HOH A:2178BINDING SITE FOR RESIDUE GOL A1422

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.SYT1_RAT156-244
286-377		  1-
A:286-377

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000488801ENSRNOE00000351650chr7:47795496-47795335162SYT1_RAT-00--
1.2ENSRNOT000000488802ENSRNOE00000347204chr7:47676650-47676550101SYT1_RAT-00--
1.3ENSRNOT000000488803ENSRNOE00000362852chr7:47593840-4759377962SYT1_RAT-00--
1.4ENSRNOT000000488804ENSRNOE00000059145chr7:47436218-47436039180SYT1_RAT1-55550--
1.5ENSRNOT000000488805ENSRNOE00000059311chr7:47390137-47389953185SYT1_RAT55-116620--
1.6ENSRNOT000000488806ENSRNOE00000059473chr7:47384355-47384233123SYT1_RAT117-157410--
1.7ENSRNOT000000488807ENSRNOE00000059587chr7:47379588-47379421168SYT1_RAT158-213560--
1.8ENSRNOT000000488808ENSRNOE00000364413chr7:47376456-47376289168SYT1_RAT214-269560--
1.9ENSRNOT000000488809ENSRNOE00000306315chr7:47330574-47330457118SYT1_RAT270-309401A:270-30940
1.10ENSRNOT0000004888010ENSRNOE00000059906chr7:47247255-47247122134SYT1_RAT309-353451A:309-35345
1.11ENSRNOT0000004888011ENSRNOE00000317890chr7:47243869-47243375495SYT1_RAT354-421681A:354-41966

(-) Sequences/Alignments

Asymmetric/Biological 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:150
 aligned with SYT1_RAT | P21707 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:150
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
             SYT1_RAT   270 QEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV 419
               SCOP domains d1uova_ A: Synaptogamin I                                                                                                                              SCOP domains
               CATH domains 1uovA00 A:270-419 C2- domain Calcium/lipid binding domain                                                                                              CATH domains
               Pfam domains -------------------C2-1uovA01 A:289-377                                                                     ------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeee....eeeeeeeeee............eeeeeeeee..eeeeeee..........eeeeeeeee....hhhh.eeeeeeee........eeeeeeee...hhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------C2  PDB: A:286-377 UniProt: 286-377                                                         ------------------------------------------ PROSITE
           Transcript 1 (1) ---------------------------------------Exon 1.10  PDB: A:309-353 UniProt: 309-353   Exon 1.11  PDB: A:354-419 UniProt: 354-421 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:270-309                -------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1uov A 270 LEKLGDICFSLRYVPTAGKLTVVILEAKNLKKMDVGGLSDPYVKIHLMQNGKRLKKKKTTIKKNTLNPYYNESFSFEVPFEQIQKVQVVVTVLDYDKIGKNDAIGKVFVGYNSTGAELRHWSDMLANPRRPIAQWHTLQVEEEVDAMLAV 419
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: C2 (71)

(-) Gene Ontology  (56, 56)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYT1_RAT | P21707)
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:0048306    calcium-dependent 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), in the presence of calcium.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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.
    GO:0017075    syntaxin-1 binding    Interacting selectively and non-covalently with the SNAP receptor syntaxin-1.
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:0071277    cellular response to calcium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0005513    detection of calcium ion    The series of events in which a calcium ion stimulus is received by a cell and converted into a molecular signal.
    GO:0098746    fast, calcium ion-dependent exocytosis of neurotransmitter    The fast, initial phase of calcium ion-induced neurotransmitter release, via exocytosis, into the synaptic cleft. This depends on low affinity calcium sensors and typically begins a fraction of a millisecond after Ca2+ influx, and decays rapidly (1-10ms) with a decay constant of around 5-10ms. The underlying molecular mechanisms of this process are distinct from those of the later, slow phase of release.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0045956    positive regulation of calcium ion-dependent exocytosis    Any process that activates or increases the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:1903861    positive regulation of dendrite extension    Any process that activates or increases the frequency, rate or extent of dendrite extension.
    GO:0050806    positive regulation of synaptic transmission    Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
    GO:0031340    positive regulation of vesicle fusion    Any process that activates or increases the frequency, rate or extent of vesicle fusion.
    GO:0017158    regulation of calcium ion-dependent exocytosis    Any process that modulates the frequency, rate or extent of calcium ion-dependent exocytosis.
    GO:1903305    regulation of regulated secretory pathway    Any process that modulates the frequency, rate or extent of regulated secretory pathway.
    GO:0051966    regulation of synaptic transmission, glutamatergic    Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0051592    response to calcium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0048488    synaptic vesicle endocytosis    Clathrin-mediated endocytosis of presynaptic membrane that recycles synaptic vesicle membrane and its components following synaptic vesicle exocytosis. This process starts with coating of the membrane with adaptor proteins and clathrin prior to invagination and ends when uncoating has finished.
    GO:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
    GO:0048278    vesicle docking    The initial attachment of a transport vesicle membrane to the target membrane, mediated by proteins protruding from the membrane of the vesicle and the target membrane. Docking requires only that the two membranes come close enough for these proteins to interact and adhere.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0031201    SNARE complex    A protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers. One well-characterized example is the neuronal SNARE complex formed of synaptobrevin 2, syntaxin 1a, and SNAP-25.
    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:0042584    chromaffin granule membrane    The lipid bilayer surrounding a chromaffin granule, a specialized secretory vesicle found in the cells of adrenal glands and various other organs, which is concerned with the synthesis, storage, metabolism, and secretion of epinephrine and norepinephrine.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031045    dense core granule    Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted.
    GO:0060076    excitatory synapse    A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell.
    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:0043229    intracellular organelle    Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. 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: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:0042734    presynaptic membrane    A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    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.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

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  SYT1_RAT | P21707
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT1_RAT | P21707: 1byn 1k5w 1rsy 1tjm 1tjx 1uow 2yoa 4wee 5ccg 5cch 5cci 5ccj 5kj7 5kj8

(-) Related Entries Specified in the PDB File

1byn SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2-DOMAIN OF SYNAPTOTAGMIN I
1rsy SYNAPTOTAGMIN I (FIRST C2 DOMAIN) (CALB)
1tjm CRYSTALLOGRAPHIC IDENTIFICATION OF SR2+ COORDINATION SITE IN SYNAPTOTAGMIN I C2B DOMAIN
1tjx CRYSTALLOGRAPHIC IDENTIFICATION OF CA2+ COORDINATION SITES IN SYNAPTOTAGMIN I C2B DOMAIN
1uow CALCIUM BINDING DOMAIN C2B