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

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Basic information

Entry
Database: PDB / ID: 4dey
TitleCrystal structure of the Voltage Dependent Calcium Channel beta-2 Subunit in Complex With The CaV1.2 I-II Linker.
Components
  • Voltage-dependent L-type calcium channel subunit alpha-1C
  • Voltage-dependent L-type calcium channel subunit beta-2
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 / voltage-gated calcium channel activity involved in AV node cell action potential / regulation of membrane repolarization during action potential / membrane depolarization during atrial cardiac muscle cell action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of adenylate cyclase activity / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / voltage-gated calcium channel activity involved in AV node cell action potential / regulation of membrane repolarization during action potential / membrane depolarization during atrial cardiac muscle cell action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of adenylate cyclase activity / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / photoreceptor ribbon synapse / positive regulation of calcium ion transport / calcium ion transport into cytosol / calcium ion import / voltage-gated calcium channel complex / calcium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / T-tubule / visual perception / calcium ion transmembrane transport / postsynaptic density membrane / sarcolemma / actin filament binding / presynapse / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / perikaryon / postsynaptic density / calmodulin binding / dendrite / membrane / metal ion binding / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain ...Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / 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 / Voltage-dependent channel domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 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
BROMIDE ION / Voltage-dependent L-type calcium channel subunit alpha-1C / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 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: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,94419
Polymers50,5852
Non-polymers1,35817
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-19 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.257, 70.512, 134.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Voltage-dependent L-type calcium channel subunit alpha-1C / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Smooth muscle calcium ...Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Smooth muscle calcium channel blocker receptor / CACB-receptor / Voltage-gated calcium channel subunit alpha Cav1.2


Mass: 12304.416 Da / Num. of mol.: 1 / Fragment: Intracellular I-II linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P15381
#2: Protein Voltage-dependent L-type calcium channel subunit beta-2 / CAB2 / Calcium channel voltage-dependent subunit beta 2


Mass: 38280.875 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
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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 (%)
12.4950.67
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion7.51.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with KI before freezing , pH 7.5, VAPOR DIFFUSION, temperature 292K
2922vapor diffusion7.51.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with KI before freezing, pH 7.5, VAPOR DIFFUSION, temperature 292K
2923vapor diffusion7.51.1-1.25 M potassium sodium tartrate, 0.1 M Tris Soaked with NaBr before freezing, pH 7.5, VAPOR DIFFUSION, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF BM1411.24
ROTATING ANODERIGAKU21.542
SYNCHROTRONESRF BM1430.918
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 1, 2006
RIGAKU RAXIS IV2IMAGE PLATEMar 25, 2006
MARMOSAIC 225 mm CCD3CCDApr 1, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Copper AnodeSINGLE WAVELENGTHMx-ray1
3Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.241
21.5421
30.9181
ReflectionResolution: 1.95→30 Å / Num. obs: 37774 / % possible obs: 91 %
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.380.2673.71,2,388.2
2.7-2.80.3343.31,2,399.2
1.95-2.020.3381.21,2,336.7

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Processing

Software
NameClassification
PHENIXrefinement
SHARPphasing
REFMACrefinement
CNSrefinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→29.398 Å / SU ML: 0.54 / σ(F): 1.32 / Phase error: 22.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1813 4.99 %Random
Rwork0.199 ---
obs0.2006 36351 96.45 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.146 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2---0.5495 Å2-0 Å2
3----0.6305 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 17 158 2587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062481
X-RAY DIFFRACTIONf_angle_d1.033368
X-RAY DIFFRACTIONf_dihedral_angle_d15.061922
X-RAY DIFFRACTIONf_chiral_restr0.071384
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00270.36551080.35921727X-RAY DIFFRACTION64
2.0027-2.06170.34341220.26792485X-RAY DIFFRACTION91
2.0617-2.12820.28731200.22612685X-RAY DIFFRACTION99
2.1282-2.20420.26091280.20342733X-RAY DIFFRACTION100
2.2042-2.29250.2241340.18792715X-RAY DIFFRACTION100
2.2925-2.39670.22061370.18922723X-RAY DIFFRACTION100
2.3967-2.5230.2281370.20162758X-RAY DIFFRACTION100
2.523-2.6810.24041500.21112722X-RAY DIFFRACTION100
2.681-2.88790.26031450.21212728X-RAY DIFFRACTION100
2.8879-3.17820.25121400.2192766X-RAY DIFFRACTION100
3.1782-3.63730.24011460.18992778X-RAY DIFFRACTION100
3.6373-4.57980.19071650.17232804X-RAY DIFFRACTION100
4.5798-29.40130.21821810.19972914X-RAY DIFFRACTION100

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