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- PDB-1t0h: Crystal structure of the Rattus norvegicus voltage gated calcium ... -

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Basic information

Entry
Database: PDB / ID: 1t0h
TitleCrystal structure of the Rattus norvegicus voltage gated calcium channel beta subunit isoform 2a
Components(VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A) x 2
KeywordsSIGNALING PROTEIN / SH3 domain / Nucleotide kinase like domain
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of high voltage-gated calcium channel activity / membrane depolarization during atrial cardiac muscle cell action potential / regulation of presynaptic cytosolic calcium ion concentration / membrane depolarization during AV node cell action potential ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of high voltage-gated calcium channel activity / membrane depolarization during atrial cardiac muscle cell action potential / regulation of presynaptic cytosolic calcium ion concentration / membrane depolarization during AV node cell action potential / photoreceptor ribbon synapse / L-type voltage-gated calcium channel complex / positive regulation of calcium ion transport / high voltage-gated calcium channel activity / calcium ion import / neuromuscular junction development / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / calcium channel regulator activity / voltage-gated calcium channel activity / visual perception / protein localization to plasma membrane / phosphoprotein binding / calcium ion transmembrane transport / calcium ion transport / actin filament binding / presynapse / chemical synaptic transmission / protein domain specific binding / protein kinase binding / identical protein binding
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. / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsVan Petegem, F. / Clark, K. / Chatelain, F. / Minor Jr., D.
CitationJournal: Nature / Year: 2004
Title: Structure of a complex between a voltage-gated calcium channel beta-subunit and an alpha-subunit domain.
Authors: Van Petegem, F. / Clark, K.A. / Chatelain, F.C. / Minor, D.L.
History
DepositionApr 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
B: VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7763
Polymers40,7402
Non-polymers351
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-15 kcal/mol
Surface area16070 Å2
MethodPISA
2
A: VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A
hetero molecules

B: VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A


Theoretical massNumber of molelcules
Total (without water)40,7763
Polymers40,7402
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.176, 45.260, 58.701
Angle α, β, γ (deg.)107.34, 95.75, 97.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A /


Mass: 15137.462 Da / Num. of mol.: 1 / Fragment: residues 17-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CACNB2 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8VGC3
#2: Protein VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT BETA2A /


Mass: 25602.660 Da / Num. of mol.: 1 / Fragment: residues 203-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CACNB2 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8VGC3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.3 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-Cl, NaCl, PEG 4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0199, 0.9796
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2004
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01991
20.97961
ReflectionResolution: 1.97→30 Å / Num. all: 24274 / Num. obs: 24274 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.19 % / Biso Wilson estimate: 31.255 Å2 / Rsym value: 0.069 / Net I/σ(I): 27.51
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2.17 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 2402 / Rsym value: 0.305 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.97→55.05 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.383 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21321 1214 5 %RANDOM
Rwork0.18547 ---
obs0.18693 22945 97.83 %-
all-24274 --
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: 23.714 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.31 Å20.32 Å2
2---0.41 Å2-0.4 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.97→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 1 148 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222270
X-RAY DIFFRACTIONr_bond_other_d0.0020.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9593074
X-RAY DIFFRACTIONr_angle_other_deg0.8434903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655277
X-RAY DIFFRACTIONr_chiral_restr0.0850.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022467
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02435
X-RAY DIFFRACTIONr_nbd_refined0.2120.2434
X-RAY DIFFRACTIONr_nbd_other0.240.22356
X-RAY DIFFRACTIONr_nbtor_other0.0880.21338
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2128
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.211
X-RAY DIFFRACTIONr_mcbond_it0.9111.51420
X-RAY DIFFRACTIONr_mcangle_it1.74422297
X-RAY DIFFRACTIONr_scbond_it2.9833850
X-RAY DIFFRACTIONr_scangle_it4.9884.5777
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 87
Rwork0.222 1693

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