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- PDB-1t3s: Structural Analysis of the Voltage-Dependent Calcium Channel Beta... -

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Basic information

Entry
Database: PDB / ID: 1t3s
TitleStructural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core
ComponentsDihydropyridine-sensitive L-type, calcium channel beta-2 subunit
KeywordsTRANSPORT PROTEIN / SH3 DOMAIN / GUANYLATE KINASE DOMAIN
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 / 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 / positive regulation of calcium ion transport / calcium ion import / regulation of heart rate by cardiac conduction / visual perception ...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 / 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 / positive regulation of calcium ion transport / calcium ion import / regulation of heart rate by cardiac conduction / visual perception / actin filament binding / presynapse / chemical synaptic transmission
Similarity search - Function
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 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / SH3 type barrels. ...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 / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsOpatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A.
Citation
Journal: Neuron / Year: 2004
Title: Structural analysis of the voltage-dependent calcium channel beta subunit functional core and its complex with the alpha 1 interaction domain.
Authors: Opatowsky, Y. / Chen, C.C. / Campbell, K.P. / Hirsch, J.A.
#1: Journal: To be published
Title: Expression, Purification and Crystallization of a Functional Core of the Voltage-Dependent Calcium Channel Beta Subunit
Authors: Opatowsky, Y. / Chomsky-Hecht, O. / Hirsch, J.A.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 12, 2014Group: Database references
Revision 1.4Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT P54288, ISOFORM 2A. RESIDUES 138-141 IN THE ...SEQUENCE THE SEQUENCE OF THE PROTEIN IS FROM SWISSPROT 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5422
Polymers38,3411
Non-polymers2011
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.066, 163.841, 34.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit / Voltage-Dependent Calcium Channel Beta-2 Subunit / CAB2


Mass: 38340.953 Da / Num. of mol.: 1 / Fragment: Functional Core (Residues 25-422) / Mutation: P122R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNB2, CACNLB2 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54288
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20K, BICINE, SODIUM CHLORIDE, BETA-MERCAPTOETHANOL, MPD, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18271 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.4
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.3 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: model built from earlier MAD data

Resolution: 2.3→81.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.912 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27728 935 5.1 %RANDOM
Rwork0.26147 ---
obs0.26222 17294 92.79 %-
all-18229 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.757 Å2
Baniso -1Baniso -2Baniso -3
1--3.86 Å20 Å20 Å2
2--5.23 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 1 87 2370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212327
X-RAY DIFFRACTIONr_bond_other_d00.022148
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9523159
X-RAY DIFFRACTIONr_angle_other_deg3.50634994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2135291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022580
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02449
X-RAY DIFFRACTIONr_nbd_refined0.2410.2652
X-RAY DIFFRACTIONr_nbd_other0.3020.22542
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1090.21174
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.5591.51476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.70522377
X-RAY DIFFRACTIONr_scbond_it2.3233851
X-RAY DIFFRACTIONr_scangle_it3.4924.5782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 70
Rwork0.377 1168

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