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- PDB-4dex: Crystal structure of the Voltage Dependent Calcium Channel beta-2... -

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Basic information

Entry
Database: PDB / ID: 4dex
TitleCrystal structure of the Voltage Dependent Calcium Channel beta-2 Subunit in Complex With The CaV2.2 I-II Linker.
Components
  • Voltage-dependent L-type calcium channel subunit beta-2
  • Voltage-dependent N-type calcium channel subunit alpha-1B
KeywordsTRANSPORT PROTEIN / MAGUK / Voltage Dependent Calcium Channel
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Presynaptic depolarization and calcium channel opening / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / : / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / neurotransmitter secretion / positive regulation of calcium ion transport ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Presynaptic depolarization and calcium channel opening / voltage-gated calcium channel activity involved in AV node cell action potential / membrane depolarization during atrial cardiac muscle cell action potential / : / high voltage-gated calcium channel activity / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / neurotransmitter secretion / positive regulation of calcium ion transport / calcium ion import / regulation of monoatomic ion transmembrane transport / positive regulation of neurotransmitter secretion / voltage-gated calcium channel complex / regulation of heart contraction / response to pain / response to testosterone / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / response to amyloid-beta / voltage-gated calcium channel activity / axon terminus / sensory perception of pain / visual perception / protein phosphatase 2A binding / dendritic shaft / locomotory behavior / calcium ion transmembrane transport / modulation of chemical synaptic transmission / response to organic cyclic compound / regulation of blood pressure / calcium ion transport / actin filament binding / presynapse / chemical synaptic transmission / response to ethanol / neuron projection / neuronal cell body / calcium ion binding / dendrite / protein-containing complex / ATP binding / membrane / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2500 / Voltage-dependent calcium channel, N-type, alpha-1 subunit / Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2500 / Voltage-dependent calcium channel, N-type, alpha-1 subunit / Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage-dependent calcium channel, L-type, beta subunit / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Voltage-dependent channel domain superfamily / Helix non-globular / Special / SH3 type barrels. / Src homology 3 domains / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / Ion transport domain / Ion transport protein / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Voltage-dependent L-type calcium channel subunit beta-2 / Voltage-dependent N-type calcium channel subunit alpha-1B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsAlmagor, L. / Hirsch, J.A.
CitationJournal: J.Neurosci. / Year: 2012
Title: The role of a voltage-dependent Ca2+ channel intracellular linker: a structure-function analysis.
Authors: Almagor, L. / Chomsky-Hecht, O. / Ben-Mocha, A. / Hendin-Barak, D. / Dascal, N. / Hirsch, J.A.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit beta-2
B: Voltage-dependent N-type calcium channel subunit alpha-1B


Theoretical massNumber of molelcules
Total (without water)51,5442
Polymers51,5442
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-13 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.908, 68.661, 79.158
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Voltage-dependent L-type calcium channel subunit beta-2 / CAB2 / Calcium channel voltage-dependent subunit beta 2


Mass: 38425.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNB2, CACNLB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P54288
#2: Protein Voltage-dependent N-type calcium channel subunit alpha-1B / Brain calcium channel III / BIII / Calcium channel / L type / alpha-1 polypeptide isoform 5 / ...Brain calcium channel III / BIII / Calcium channel / L type / alpha-1 polypeptide isoform 5 / Voltage-gated calcium channel subunit alpha Cav2.2


Mass: 13118.750 Da / Num. of mol.: 1 / Fragment: Intracellular I-II linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cach5, Cacna1b, Cacnl1a5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02294
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THE PROTEIN IS FROM UNP P54288, ISOFORM 2A. RESIDUES 138-141 IN THE COORDINATES ...THE SEQUENCE OF THE PROTEIN IS FROM UNP P54288, ISOFORM 2A. RESIDUES 138-141 IN THE COORDINATES WERE INTRODUCED INTO THE PROTEIN. THEY REPLACE RESIDUES 138-202 FROM THE NATIVE SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.935.24
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion80.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 , pH 8.0, VAPOR DIFFUSION, temperature 292K
2922vapor diffusion80.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K
2923vapor diffusion80.1 M NaCl, 0.1 M Bicine, 23-26% PEG 400 Soaked with NaBr before freezing, pH 8.0, VAPOR DIFFUSION, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.873
SYNCHROTRONESRF BM1420.918
SYNCHROTRONESRF BM1430.918
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 2, 2006
MARMOSAIC 225 mm CCD2CCDApr 1, 2006
MARMOSAIC 225 mm CCD3CCDApr 1, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1horizontally side diffracting Silicon 111 crystal (fixed wavelength)SINGLE WAVELENGTHMx-ray1
2Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
3Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
20.9181
ReflectionResolution: 2→30 Å / Num. all: 26222 / Num. obs: 26222 / % possible obs: 90.1 %
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.070.4211.71,2,353.6
2.4-2.490.2392.91,2,355.1
2.4-2.490.2272.81,2,351.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2→27.313 Å / SU ML: 0.52 / σ(F): 0 / Phase error: 24.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1236 5.19 %RANDOM
Rwork0.1975 ---
obs0.1996 23818 90.94 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.052 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5628 Å20 Å2-0.2462 Å2
2---2.1694 Å2-0 Å2
3---1.6066 Å2
Refinement stepCycle: LAST / Resolution: 2→27.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 0 162 2826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082715
X-RAY DIFFRACTIONf_angle_d1.0323670
X-RAY DIFFRACTIONf_dihedral_angle_d16.7281035
X-RAY DIFFRACTIONf_chiral_restr0.069412
X-RAY DIFFRACTIONf_plane_restr0.004479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.2762900.26751493X-RAY DIFFRACTION55
2.0801-2.17470.2705990.24212199X-RAY DIFFRACTION79
2.1747-2.28930.28981370.23492512X-RAY DIFFRACTION91
2.2893-2.43270.25541290.21832608X-RAY DIFFRACTION95
2.4327-2.62040.241590.20652691X-RAY DIFFRACTION98
2.6204-2.88380.26511650.20412732X-RAY DIFFRACTION100
2.8838-3.30050.21981450.19382763X-RAY DIFFRACTION100
3.3005-4.15590.25221560.17922761X-RAY DIFFRACTION100
4.1559-27.3160.21191560.19082823X-RAY DIFFRACTION100

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