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(-) Description

Title :  THE RIM1ALPHA C2B DOMAIN
 
Authors :  R. Guan, H. Dai, D. R. Tomchick, M. Machius, T. C. Sudhof, J. Rizo
Date :  30 May 07  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C2 Domain Dimer, Neurotransmitter Release, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Guan, H. Dai, D. R. Tomchick, I. Dulubova, M. Machius, T. C. Sudhof, J. Rizo
Crystal Structure Of The Rim1Alpha C(2)B Domain At 1. 7 A Resolution.
Biochemistry V. 46 8988 2007
PubMed-ID: 17630786  |  Reference-DOI: 10.1021/BI700698A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-KT
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentC2B DOMAIN
    GeneRIMS1, RIM1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRAB3-INTERACTING MOLECULE 1, RIM 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4SO47Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:23 , LYS A:1501 , TYR A:1503 , LYS A:1513 , LYS A:1556 , ARG B:1454 , GLN B:1455 , ASP B:1589BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWAREHOH A:138 , ARG A:1454 , GLN A:1455 , ASP A:1589 , LYS B:1501 , TYR B:1503 , LYS B:1513 , LYS B:1556BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWARETYR A:1499 , LYS A:1501 , LYS A:1515 , LYS A:1556BINDING SITE FOR RESIDUE SO4 A 204
04AC4SOFTWAREARG A:1482 , ARG A:1484 , GLN B:1538BINDING SITE FOR RESIDUE SO4 A 206
05AC5SOFTWAREHOH A:58 , HOH A:164 , ARG A:1520 , THR A:1522 , GLN A:1538BINDING SITE FOR RESIDUE SO4 A 207
06AC6SOFTWAREPRO A:1584 , SER A:1585BINDING SITE FOR RESIDUE CL A 402
07AC7SOFTWARESER A:1536 , LYS A:1540BINDING SITE FOR RESIDUE CL A 403
08AC8SOFTWAREHOH A:1 , GLN A:1466 , ARG A:1482 , TRP A:1578 , HOH B:77 , HOH B:183 , GLU B:1535 , SER B:1536 , LYS B:1540BINDING SITE FOR RESIDUE SO4 B 203
09AC9SOFTWARETYR B:1499 , LYS B:1501 , LYS B:1515 , LYS B:1556BINDING SITE FOR RESIDUE SO4 B 205
10BC1SOFTWAREHOH A:90 , ASP B:1534 , GLU B:1535BINDING SITE FOR RESIDUE NA B 301
11BC2SOFTWAREHOH B:113 , ALA B:1458 , LYS B:1580BINDING SITE FOR RESIDUE CL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q3X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q3X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q3X)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.RIMS1_RAT769-864
1475-1563
 
  2-
A:1475-1563
B:1475-1563

(-) Exons   (0, 0)

(no "Exon" information available for 2Q3X)

(-) 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:142
 aligned with RIMS1_RAT | Q9JIR4 from UniProtKB/Swiss-Prot  Length:1615

    Alignment length:174
                                  1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590    
           RIMS1_RAT   1421 SSEGNLIFPGVRVGPDSQFSDFLDGLGPAQLVGRQTLATPAMGDIQIGMEDKKGQLEVEVIRARSLTQKPGSKSTPAPYVKVYLLENGACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDYGRMDHKCFMGVAQILLEELDLSSMVIGWYKLFPPSSLVDPTLAP 1594
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..------------------------...eeee..-----...eeeeeeeee..eeeeeeeeee......---...eeeeeeeeee..eeeeeee..........eeeeeee.......eeeeeeeeee.......eeeeeeee.hhhh.....eeeeee..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------C2  PDB: A:1475-1563 UniProt: 1475-1563                                                  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2q3x A 1445 SP------------------------GPAQLVGRQ-----AmGDIQIGmEDKKGQLEVEVIRARSLTQKP---STPAPYVKVYLLENGACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDYGRmDHKCFmGVAQILLEELDLSSmVIGWYKLFPPSSLVDPTLAP 1594
                             |       -         -      1450    |    -||    1470      1480      1490   |  1500      1510      1520      1530      1540      1550  |   1560      1570   |  1580      1590    
                             |                     1447    1455  1461|      |                 1490   |                                                       1553-MSE |           1574-MSE                
                          1446                                    1462-MSE  |                     1494                                                             1559-MSE                               
                                                                         1469-MSE                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with RIMS1_RAT | Q9JIR4 from UniProtKB/Swiss-Prot  Length:1615

    Alignment length:174
                                  1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530      1540      1550      1560      1570      1580      1590    
           RIMS1_RAT   1421 SSEGNLIFPGVRVGPDSQFSDFLDGLGPAQLVGRQTLATPAMGDIQIGMEDKKGQLEVEVIRARSLTQKPGSKSTPAPYVKVYLLENGACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDYGRMDHKCFMGVAQILLEELDLSSMVIGWYKLFPPSSLVDPTLAP 1594
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --                        -----------------------------C2-2q3xB01 B:14   76-1563                                                               ------------------------------- Pfam domains (1)
           Pfam domains (2) --                        -----------------------------C2-2q3xB02 B:14   76-1563                                                               ------------------------------- Pfam domains (2)
         Sec.struct. author ..------------------------...eeee..........eeeeeeeee..eeeeeeeeee......---...eeeeeeeeee..eeeeeee..........eeeeeee.......eeeeeeeeee.---...eeeeeeeee.hhh.....eeeeee..hhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------C2  PDB: B:1475-1563 UniProt: 1475-1563                                                  ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2q3x B 1445 SP------------------------GPAQLVGRQTLATPAmGDIQIGmEDKKGQLEVEVIRARSLTQKP---STPAPYVKVYLLENGACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDY---DHKCFmGVAQILLEELDLSSmVIGWYKLFPPSSLVDPTLAP 1594
                             |       -         -      1450      1460 |    1470      1480      1490   |  1500      1510      1520      1530      1540      1550   |  1560      1570   |  1580      1590    
                          1446                     1447           1462-MSE  |                 1490   |                                                    1550   |    |           1574-MSE                
                                                                         1469-MSE                 1494                                                        1554    |                                   
                                                                                                                                                                   1559-MSE                               

   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  (0, 0)

(no "SCOP Domain" information available for 2Q3X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q3X)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: C2 (71)
(-)
Family: C2 (34)
1aC2-2q3xB01B:1476-1563
1bC2-2q3xB02B:1476-1563

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIMS1_RAT | Q9JIR4)
molecular function
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
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: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:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic 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:0006836    neurotransmitter transport    The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0097151    positive regulation of inhibitory postsynaptic potential    Any process that activates or increases the frequency, rate or extent of inhibitory postsynaptic potential (IPSP). IPSP is a temporary decrease in postsynaptic membrane potential due to the flow of negatively charged ions into the postsynaptic cell. The flow of ions that causes an IPSP is an inhibitory postsynaptic current (IPSC) and makes it more difficult for the neuron to fire an action potential.
    GO:0031632    positive regulation of synaptic vesicle fusion to presynaptic active zone membrane    Any process that activates or increases the frequency, rate or extent of synaptic vesicle fusion to the presynaptic membrane.
    GO:0010808    positive regulation of synaptic vesicle priming    Any process that increases the frequency, rate or extent of synaptic vesicle priming. Synaptic vesicle priming is the formation of SNARE-containing complexes, bringing synaptic vesicle membrane and plasma membranes into close proximity and thereby facilitating membrane fusion.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0048786    presynaptic active zone    A specialized region of the plasma membrane and cell cortex of a presynaptic neuron; encompasses a region of the plasma membrane where synaptic vesicles dock and fuse, and a specialized cortical cytoskeletal matrix.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIMS1_RAT | Q9JIR41zub

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