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- PDB-1t3l: Structural Analysis of the Voltage-Dependent Calcium Channel Beta... -

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Basic information

Entry
Database: PDB / ID: 1t3l
TitleStructural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional Core in Complex with Alpha1 Interaction Domain
Components
  • Dihydropyridine-sensitive L-type, calcium channel beta-2 subunit
  • Voltage-dependent L-type calcium channel alpha-1S subunit
KeywordsTRANSPORT PROTEIN / protein-peptide complex / 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 / positive regulation of muscle contraction / 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 / cellular response to caffeine ...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 / positive regulation of muscle contraction / 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 / cellular response to caffeine / calcium ion import across plasma membrane / regulation of heart rate by cardiac conduction / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / muscle contraction / release of sequestered calcium ion into cytosol / T-tubule / visual perception / calcium ion transmembrane transport / actin filament binding / presynapse / chemical synaptic transmission / transmembrane transporter binding / calmodulin binding / 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-1S subunit / 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-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, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1S subunit / 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-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
Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOpatowsky, Y. / Chen, C.-C. / Campbell, K.P. / Hirsch, J.A.
Citation
Journal: NEURON / Year: 2004
Title: Structural Analysis of Voltage-Dependent Calcium Channel Beta Subunit Functional Core and Its Complex with the Alpha1 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 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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
B: Voltage-dependent L-type calcium channel alpha-1S subunit


Theoretical massNumber of molelcules
Total (without water)40,5252
Polymers40,5252
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.775, 168.262, 34.233
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: Protein/peptide Voltage-dependent L-type calcium channel alpha-1S subunit / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle


Mass: 2184.363 Da / Num. of mol.: 1 / Fragment: AID / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is from Oryctolagus cuniculus (rabbit) gene CACNA1S.
References: UniProt: P07293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20K, Bicine, sodium chloride, beta-mercaptoethanol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0069 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0069 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19123 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.3
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.9 / % possible all: 63.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→84.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.447 / SU ML: 0.186 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28201 1283 6.9 %RANDOM
Rwork0.22138 ---
obs0.22554 17364 83.77 %-
all-18647 --
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: 42.992 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2--3.7 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 128 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212594
X-RAY DIFFRACTIONr_bond_other_d0.0030.022390
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9553513
X-RAY DIFFRACTIONr_angle_other_deg0.85835568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585320
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_restr0.0990.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022859
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02500
X-RAY DIFFRACTIONr_nbd_refined0.2220.2657
X-RAY DIFFRACTIONr_nbd_other0.2520.22884
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4850.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.011.51621
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91822618
X-RAY DIFFRACTIONr_scbond_it2.5543973
X-RAY DIFFRACTIONr_scangle_it4.2534.5895
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 60
Rwork0.258 858

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