Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIM2 C2A-DOMAIN AT 1.4 ANGSTROM RESOLUTION
 
Authors :  H. Dai, D. R. Tomchick, J. Garcia, T. C. Sudhof, M. Machius, J. Rizo
Date :  15 Jul 05  (Deposition) - 20 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  C2 Domain, Neurotransmitter Release, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Dai, D. R. Tomchick, J. Garcia, T. C. Sudhof, M. Machius, J. Rizo
Crystal Structure Of The Rim2 C(2)A-Domain At 1. 4 A Resolution.
Biochemistry V. 44 13533 2005
PubMed-ID: 16216076  |  Reference-DOI: 10.1021/BI0513608

(-) Compounds

Molecule 1 - REGULATING SYNAPTIC MEMBRANE EXOCYTOSIS PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentC2 DOMAIN, RESIDUES 725-853
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymRAB3-INTERACTING MOLECULE, 2RIM2 C2A DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:742 , HIS A:804 , ARG A:805 , ARG A:806 , HOH A:2024 , HOH A:2110BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREARG A:806 , HOH A:2111BINDING SITE FOR RESIDUE SO4 A 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:772 -Pro A:773
2Ser A:801 -Pro A:802

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C2PS50004 C2 domain profile.RIMS2_RAT756-851
1415-1503
  1A:740-835
-

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000507531ENSRNOE00000454594chr7:74757003-74757229227RIMS2_RAT1-59590--
1.4ENSRNOT000000507534ENSRNOE00000223871chr7:74862495-74862705211RIMS2_RAT59-129710--
1.5ENSRNOT000000507535ENSRNOE00000223852chr7:74922056-74922366311RIMS2_RAT130-2331040--
1.7ENSRNOT000000507537ENSRNOE00000245525chr7:75007836-75008761926RIMS2_RAT233-5423100--
1.8ENSRNOT000000507538ENSRNOE00000236412chr7:75022293-7502236068RIMS2_RAT542-564230--
1.10ENSRNOT0000005075310ENSRNOE00000309334chr7:75024249-75024368120RIMS2_RAT565-604400--
1.11ENSRNOT0000005075311ENSRNOE00000313303chr7:75026216-75026315100RIMS2_RAT605-638340--
1.12ENSRNOT0000005075312ENSRNOE00000342737chr7:75027291-75027414124RIMS2_RAT638-679420--
1.13ENSRNOT0000005075313ENSRNOE00000310460chr7:75029686-7502973247RIMS2_RAT679-695170--
1.14ENSRNOT0000005075314ENSRNOE00000300188chr7:75032477-75032589113RIMS2_RAT695-732381A:725-7328
1.15ENSRNOT0000005075315ENSRNOE00000328054chr7:75038397-7503844448RIMS2_RAT733-748160--
1.16ENSRNOT0000005075316ENSRNOE00000236330chr7:75041602-75041732131RIMS2_RAT749-792441A:733-77644
1.17ENSRNOT0000005075317ENSRNOE00000236358chr7:75048205-75048376172RIMS2_RAT792-849581A:776-833 (gaps)58
1.18ENSRNOT0000005075318ENSRNOE00000236351chr7:75050571-75050724154RIMS2_RAT850-901521A:834-85320
1.19ENSRNOT0000005075319ENSRNOE00000236324chr7:75081091-7508115969RIMS2_RAT901-924240--
1.20ENSRNOT0000005075320ENSRNOE00000236341chr7:75090877-75091033157RIMS2_RAT924-976530--
1.21ENSRNOT0000005075321ENSRNOE00000045881chr7:75092194-75092304111RIMS2_RAT976-1013380--
1.22ENSRNOT0000005075322ENSRNOE00000329316chr7:75098602-7509866766RIMS2_RAT1013-1035230--
1.23ENSRNOT0000005075323ENSRNOE00000046081chr7:75109786-75109965180RIMS2_RAT1035-1095610--
1.24ENSRNOT0000005075324ENSRNOE00000350038chr7:75110820-75110929110RIMS2_RAT1095-1132380--
1.25ENSRNOT0000005075325ENSRNOE00000359488chr7:75130866-7513090742RIMS2_RAT1132-1146150--
1.26ENSRNOT0000005075326ENSRNOE00000223420chr7:75139420-75139520101RIMS2_RAT1146-1179340--
1.28ENSRNOT0000005075328ENSRNOE00000248632chr7:75159578-75159750173RIMS2_RAT1180-1237580--
1.30ENSRNOT0000005075330ENSRNOE00000248608chr7:75196983-75197224242RIMS2_RAT1237-1318820--
1.32aENSRNOT0000005075332aENSRNOE00000248577chr7:75250727-75250868142RIMS2_RAT1318-1365480--
1.33ENSRNOT0000005075333ENSRNOE00000321148chr7:75268338-75268450113RIMS2_RAT1365-1403390--
1.34ENSRNOT0000005075334ENSRNOE00000248520chr7:75268763-75268864102RIMS2_RAT1403-1437350--
1.35ENSRNOT0000005075335ENSRNOE00000248504chr7:75270057-75270196140RIMS2_RAT1437-1483470--
1.36ENSRNOT0000005075336ENSRNOE00000045670chr7:75270633-752717711139RIMS2_RAT1484-1555720--

(-) 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:122
 aligned with RIMS2_RAT | Q9JIS1 from UniProtKB/Swiss-Prot  Length:1555

    Alignment length:145
                                   734       744       754       764       774       784       794       804       814       824       834       844       854       864     
            RIMS2_RAT   725 QFLSGQLSSQSLSRRTTPFVPRVQIKLWFDKVGHQLIVTILGAKDLPSREDGRPRNPYVKIYFLPDRSDKNKRRTKTVKKTLEPKWNQTFIYSPVHRREFRERMLEITLWDQARVREEESEFLGEILIELETALLDDEPHWYKLQ 869
               SCOP domains d2bwqa_                 A: automated matches                                                                                                      SCOP domains
               CATH domains 2bwqA00                 A:725-853 C2- domain Calcium/lipid binding domain                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee----------------eeeeee....eeeeeeeeee............eeeeeeee...hhh.eee..........eeeeeeee...hhhhhhh.eeeeeeee.-------.eeeeeeeee.hhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------C2  PDB: A:740-835 UniProt: 756-851                                                             ------------------ PROSITE
           Transcript 1 (1) 1.14    Exon 1.15  PDB: Exon 1.16  PDB: A:733-776 UniProt: 749-792  ---------------------------------------------------------Exon 1.18            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.17  PDB: A:776-833 (gaps) UniProt: 792-849         -------------------- Transcript 1 (2)
                 2bwq A 725 QFLSGQLS----------------IKLWFDKVGHQLIVTILGAKDLPSREDGRPRNPYVKIYFLPDRSDKNKRRTKTVKKTLEPKWNQTFIYSPVHRREFRERMLEITLWDQ-------SEFLGEILIELETALLDDEPHWYKLQ 853
                                   | -         -    |  738       748       758       768       778       788       798       808       818 |     828       838       848     
                                 732              733                                                                                    820     828                         

   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  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BWQ)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIMS2_RAT | Q9JIS1)
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:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    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: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.
biological process
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    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:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    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: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:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0042391    regulation of membrane potential    Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:0061669    spontaneous neurotransmitter secretion    Neurotransmitter secretion that occurs in the absence of the action of a secretagogue or a presynaptic action potential.
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:772 - Pro A:773   [ RasMol ]  
    Ser A:801 - Pro A:802   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2bwq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RIMS2_RAT | Q9JIS1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RIMS2_RAT | Q9JIS1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RIMS2_RAT | Q9JIS12a20 2cjs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BWQ)