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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RATTUS NORVEGICUS VOLTAGE GATED CALCIUM CHANNEL BETA SUBUNIT ISOFORM 2A
 
Authors :  F. Van Petegem, K. Clark, F. Chatelain, D. Minor Jr.
Date :  08 Apr 04  (Deposition) - 15 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Sh3 Domain, Nucleotide Kinase Like Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Van Petegem, K. A. Clark, F. C. Chatelain, D. L. Minor
Structure Of A Complex Between A Voltage-Gated Calcium Channel Beta-Subunit And An Alpha-Subunit Domain.
Nature V. 429 671 2004
PubMed-ID: 15141227  |  Reference-DOI: 10.1038/NATURE02588
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 17-145
    Gene: CACNB2
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 2 - VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 203-425
    Gene: CACNB2
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:131 , ARG A:134 , HOH B:56 , HOH B:92 , ILE B:287BINDING SITE FOR RESIDUE CL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0H)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.CACB2_RAT110-171  1A:59-120
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.CACB2_RAT110-171  1A:59-120
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.CACB2_RAT110-171  1A:59-120

(-) Exons   (0, 0)

(no "Exon" information available for 1T0H)

(-) Sequences/Alignments

Asymmetric 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:96
 aligned with CACB2_RAT | Q8VGC3 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:96
                                   101       111       121       131       141       151       161       171       181      
            CACB2_RAT    92 RREAERQAQAQLEKAKTKPVAFAVRTNVRYSAAQEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENMRLQHEQRAK 187
               SCOP domains d1t0ha_ A: SH3-like domain of the L-type calcium channel                                         SCOP domains
               CATH domains 1t0hA00 A:41-136 SH3 Domains                                                                     CATH domains
               Pfam domains VGCC_beta4Aa_N-1t0------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....eeeee......hhhhh..............eeeeeee....eeeeee.......eeeehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------SH3  PDB: A:59-120 UniProt: 110-171                           ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1t0h A  41 RREAERQAQAQLEKAKTKPVAFAVRTNVRYSAAQEDDVPVPGmAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENmRLQHEQRAK 136
                                    50        60        70        80  |     90       100       110       120      |130      
                                                                     83-MSE                                     127-MSE     


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with CACB2_RAT | Q8VGC3 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:219
                                   267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467         
            CACB2_RAT   258 RMPFFKKTEHTPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIIVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPQESFDVILDENQLEDACEHLADYLEAYWKATHPPSSNLPNPLLSRT 476
               SCOP domains d1t0      hb_ B: Guanylate kinase-like domain of the L-type calcium           channel                                                                                                                                       SCOP domains
               CATH domains 1t0h      B00 B:207-425 P-loop containing nucleotide triphosphate hy          drolases                                                                                                                                      CATH domains
               Pfam domains ----      --------Guanylate_kin-1t0hB01 B:225-406                                                                                                                                                       -------          -- Pfam domains
         Sec.struct. author ....------...eeee.....eeee......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhh.----------..........hhhhhhhhhhhhhhhhh...eeeeee....hhhhh.......eeeee...hhhhhhhhhhhh------hhhhhhhhhhhhhh.hhhhhh.eee...hhhhhhhhhhhhhhhhhhhhh..----------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0h B 207 RmPF------TPPYDVVPSmRPVVLVGPSLKGYEVTDmmQKALFDFLKHRFEGRISITRVTADISLAK----------AIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIIVYVKISSPKVLQRLIKSR------HLNVQmVAADKLAQCPPQESFDVILDENQLEDACEHLADYLEAYWKATHPP----------RT 425
                             | |     -|      226       236       246       256       266       | -       286       296       306       316       326       336       346       356      |366 |     376       386       396       406      |  -       | 
                           208-MSE  217      226-MSE           244-MSE                       274        285                                                                    356    363    |                                          413        424 
                             210                                245-MSE                                                                                                                    368-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  (2, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CACB2_RAT | Q8VGC3)
molecular function
    GO:0051015    actin filament binding    Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
    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:0005246    calcium channel regulator activity    Modulates the activity of a calcium channel.
    GO:0008331    high voltage-gated calcium channel activity    Enables the transmembrane transfer of a calcium ion by a high voltage-gated channel. A high voltage-gated channel is a channel whose open state is dependent on high voltage across the membrane in which it is embedded.
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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: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.
    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:0086056    voltage-gated calcium channel activity involved in AV node cell action potential    Enables the transmembrane transfer of a calcium ion by a voltage-gated channel across the plasma membrane of an AV node cardiac muscle cell that contributes to the depolarization phase of an action potential. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
    GO:0086007    voltage-gated calcium channel activity involved in cardiac muscle cell action potential    Enables the transmembrane transfer of a calcium ion by a voltage-gated channel across the plasma membrane of a cardiac muscle cell that contributes to the depolarization phase of an action potential. 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: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:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    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:0086045    membrane depolarization during AV node cell action potential    The process in which AV node cardiac muscle cell membrane potential changes in the depolarizing direction from the negative resting potential towards the positive membrane potential that will be the peak of the action potential.
    GO:0098912    membrane depolarization during atrial cardiac muscle cell action potential    The process in which atrial cardiac muscle cell membrane potential changes in the depolarizing direction from the negative resting potential towards the positive membrane potential that will be the peak of the action potential.
    GO:0007528    neuromuscular junction development    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction.
    GO:1904879    positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel    Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transport via high voltage-gated calcium channel.
    GO:1901843    positive regulation of high voltage-gated calcium channel activity    Any process that activates or increases the frequency, rate or extent of high voltage-gated calcium channel activity.
    GO:0086091    regulation of heart rate by cardiac conduction    A cardiac conduction process that modulates the frequency or rate of heart contraction.
    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:1901385    regulation of voltage-gated calcium channel activity    Any process that modulates the frequency, rate or extent of voltage-gated calcium channel activity.
    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.

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 Related Entries

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UniProtKB/Swiss-Prot
        CACB2_RAT | Q8VGC3: 1t0j 3jbr

(-) Related Entries Specified in the PDB File

1t0j