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 :  STRUCTURAL ANALYSIS OF THE VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA SUBUNIT FUNCTIONAL CORE
 
Authors :  Y. Opatowsky, C. -C. Chen, K. P. Campbell, J. A. Hirsch
Date :  27 Apr 04  (Deposition) - 25 May 04  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Sh3 Domain, Guanylate Kinase Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Opatowsky, C. C. Chen, K. P. Campbell, J. A. Hirsch
Structural Analysis Of The Voltage-Dependent Calcium Channe Beta Subunit Functional Core And Its Complex With The Alpha 1 Interaction Domain.
Neuron V. 42 387 2004
PubMed-ID: 15134636  |  Reference-DOI: 10.1093/HMG/DDH162
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDROPYRIDINE-SENSITIVE L-TYPE, CALCIUM CHANNEL BETA-2 SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FUNCTIONAL CORE (RESIDUES 25-422)
    Gene: CACNB2, CACNLB2
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA-2 SUBUNIT, CAB2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1HG1Ligand/IonMERCURY (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:114BINDING SITE FOR RESIDUE HG A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T3S)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:218 -Pro A:219
2Gly A:234 -Pro A:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T3S)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.CACB2_RABIT86-147  1A:60-121

(-) Exons   (0, 0)

(no "Exon" information available for 1T3S)

(-) 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:294
 aligned with CACB2_RABIT | P54288 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:381
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440 
          CACB2_RABIT    61 EEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVSYSAAHEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENMRLQHEQRAKQGKFYSSKSGGNSSSSLGDIVPSSRKSTPPSSAIDIDATGLDAEENDIPANHRSPKPSANSVTSPHSKEKRMPFFKKTEHTPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIVVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPELFDVILDENQLEDACEHLADYLEAYWKATHPPSS 441
               SCOP domains d1t3sa1 A:35-141 SH3-like domain of the L-type calcium channel                                                                                                                         d1t3sa2 A:218-415 Guanylate kinase-like domain of the L-type cal           cium channel                                                                                                                SCOP domains
               CATH domains 1t3sA01 A:35-140,A:218-225 SH3 Domains                                                                    -                                                                            1t3sA01 1t3sA02 A:226-415 P-loop containing nucleotide triphosph           ate hydrolases                                                                                                              CATH domains
               Pfam domains VGCC_beta4Aa_N-1t3sA02   ----------------------------------------------------------------------------------                                                                            --------Guanylate_kin-1t3sA01 A:226-396                                                                                                                                            ------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh......eeeee.........................eeeeeee....eeeeee.......eeeehhhhhhhhhhhhhhhhhhh..----------------------------------------------------------------------------...eeee.....eeee.......hhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhh.-----------...hhhhhhhhhhhhhhhhh...eeeeee....hhhhhh......eeeee...hhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------SH3  PDB: A:60-121 UniProt: 86-147                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3s A  35 EEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVSYSAAHEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSRVKLENMRLQHEQRAKEFKL----------------------------------------------------------------------------TPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNN-----------TRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIVVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPELFDVILDENQLEDACEHLADYLEAYWKATHPPSS 415
                                    44        54        64        74        84        94       104       114       124       134      |  -         -         -         -         -         -         -         -   |   224       234       244       254       264       274      |  -       294       304       314       324       334       344       354       364       374       384       394       404       414 
                                                                                                                                    141                                                                          218                                                            281         293
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: VGCC_beta4Aa_N] (6)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CACB2_RABIT | P54288)
molecular function
    GO:0005262    calcium channel activity    Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
    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:0005245    voltage-gated calcium channel activity    Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    GO:0005244    voltage-gated ion channel activity    Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
    GO:0070588    calcium ion transmembrane transport    A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006816    calcium ion transport    The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0034765    regulation of ion transmembrane transport    Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
    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: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:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0005891    voltage-gated calcium channel complex    A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

 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
    HG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:234 - Pro A:235   [ RasMol ]  
    Thr A:218 - Pro A:219   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1t3s
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CACB2_RABIT | P54288
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CACB2_RABIT | P54288
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CACB2_RABIT | P54288: 1t3l 4dex 4dey

(-) Related Entries Specified in the PDB File

1t3l