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(-) Description

Title :  MUNC13-1 C2B-DOMAIN, CALCIUM-FREE
 
Authors :  D. R. Tomchick, J. Rizo, M. Machius, J. Lu
Date :  01 Dec 09  (Deposition) - 16 Feb 10  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Phospholipid Binding Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. H. Shin, J. Lu, J. S. Rhee, D. R. Tomchick, Z. P. Pang, S. M. Wojcik, M. Camacho-Perez, N. Brose, M. Machius, J. Rizo, C. Rosenmund, T. C. Sudhof
Munc13 C2B Domain Is An Activity-Dependent Ca2+ Regulator Of Synaptic Exocytosis.
Nat. Struct. Mol. Biol. V. 17 280 2010
PubMed-ID: 20154707  |  Reference-DOI: 10.1038/NSMB.1758
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUNC13-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KT
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC2B DOMAIN, RESIDUES 675-820
    GeneUNC-13, UNC13A, UNC13H1
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPROTEIN UNC-13 HOMOLOG A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CL2Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:18 , LYS A:722 , GLY A:730 , ARG A:754BINDING SITE FOR RESIDUE CL A 911
2AC2SOFTWAREGLN A:699BINDING SITE FOR RESIDUE CL A 912
3AC3SOFTWAREHOH A:14 , HOH A:16 , HOH A:21 , TYR A:713 , LYS A:722 , ARG A:724 , TYR A:729 , GLY A:730 , GLU A:758 , ASP A:759 , GLU A:773 , SER A:774 , ASP A:775BINDING SITE FOR RESIDUE B3P A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KWT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KWT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KWT)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.UN13A_RAT690-782
1578-1691
  1A:690-782
-

(-) Exons   (0, 0)

(no "Exon" information available for 3KWT)

(-) 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:116
 aligned with UN13A_RAT | Q62768 from UniProtKB/Swiss-Prot  Length:1735

    Alignment length:132
                                   697       707       717       727       737       747       757       767       777       787       797       807       817  
            UN13A_RAT   688 SAKISITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIKVRVLDEDDDIKSRVKQRFKRESDDFLGQTIIEVRTLSGEMDVWYNLDKRTDKSAVSGAIRLHISVEI 819
               SCOP domains d3kwta_ A: automat  ed matches                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---C2-3kwtA01 A:69  1-782                                                                      -------------------     ------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee......--....eeeeeee..eeee..........eeeeeeeeee.....eeeeeeee......---------...eeeeeeeee.hhh..eeeeeee....-----...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --C2  PDB: A:690-782 UniProt: 690-782                                                          ------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kwt A 688 SAKISITVVCAQGLQAKD--GSSDPYVTVQVGKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIKVRVLDEDDDIK---------ESDDFLGQTIIEVRTLSGEMDVWYNLDKR-----VSGAIRLHISVEI 819
                                   697       | -|      717       727       737       747       757     |   -     | 777       787       797   |   807       817  
                                           705  |                                                    763       773                         801   807            
                                              708                                                                                                               

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KWT)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UN13A_RAT | Q62768)
molecular function
    GO:0000149    SNARE binding    Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein.
    GO:0019992    diacylglycerol binding    Interacting selectively and non-covalently with diacylglycerol, a diester of glycerol and two fatty acids.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
    GO:0017075    syntaxin-1 binding    Interacting selectively and non-covalently with the SNAP receptor syntaxin-1.
biological process
    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:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0060291    long-term synaptic potentiation    A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0016082    synaptic vesicle priming    A process that converts synaptic vesicles to a state of competence for calcium triggered fusion with the active zone membrane by bringing the two membranes into very close proximity. Priming typically (but not always) occurs after docking (Jahn and Fasshauer, 2012). Primed vesicles are also capable of spontaneously fusing with the active zone membrane.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UN13A_RAT | Q627681y8f 2cjs 2cjt 2kdu 3kwu 3swh 4y21 5ue8 5uf7

(-) Related Entries Specified in the PDB File

3kwu MUNC13-1 C2B-DOMAIN, CALCIUM BOUND