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- PDB-1vyu: Beta3 subunit of Voltage-gated Ca2+-channel -

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Basic information

Entry
Database: PDB / ID: 1vyu
TitleBeta3 subunit of Voltage-gated Ca2+-channel
ComponentsCALCIUM CHANNEL BETA-3 SUBUNIT
KeywordsION TRANSPORT / CALCIUM CHANNEL BETA SUBUNIT / AID DOAMIN / IONIC CHANNEL / VOLTAGE-GATED CHANNEL / SH3 DOMAIN
Function / homology
Function and homology information


negative regulation of detection of mechanical stimulus involved in sensory perception of touch / regulation of membrane hyperpolarization / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / regulation of membrane repolarization during action potential / positive regulation of high voltage-gated calcium channel activity / calcium ion transmembrane transport via high voltage-gated calcium channel / L-type voltage-gated calcium channel complex / calcium ion transport into cytosol / voltage-gated calcium channel complex ...negative regulation of detection of mechanical stimulus involved in sensory perception of touch / regulation of membrane hyperpolarization / Presynaptic depolarization and calcium channel opening / Regulation of insulin secretion / regulation of membrane repolarization during action potential / positive regulation of high voltage-gated calcium channel activity / calcium ion transmembrane transport via high voltage-gated calcium channel / L-type voltage-gated calcium channel complex / calcium ion transport into cytosol / voltage-gated calcium channel complex / neuromuscular junction development / calcium channel regulator activity / positive regulation of excitatory postsynaptic potential / positive regulation of protein targeting to membrane / voltage-gated calcium channel activity / detection of mechanical stimulus involved in sensory perception of pain / protein localization to plasma membrane / calcium ion transmembrane transport / calcium ion transport / T cell receptor signaling pathway / cellular response to hypoxia / chemical synaptic transmission / apical plasma membrane / synapse / protein kinase binding / membrane / cytoplasm
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-3 subunit / Voltage-dependent L-type calcium channel subunit beta-3, 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-3 subunit / Voltage-dependent L-type calcium channel subunit beta-3, 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-3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsChen, Y.-H. / Li, M.-H. / Zhang, Y. / He, L.-L. / Yamada, Y. / Fitzmaurice, A. / Yang, S. / Zhang, H. / Liang, T. / Yang, J.
CitationJournal: Nature / Year: 2004
Title: Structural Basis of the Alpha(1)-Beta Subunit Interaction of Voltage-Gated Ca(2+) Channels
Authors: Chen, Y.-H. / Li, M.-H. / Zhang, Y. / He, L.-L. / Yamada, Y. / Fitzmaurice, A. / Shen, Y. / Zhang, H. / Tong, L. / Yang, J.
History
DepositionMay 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM CHANNEL BETA-3 SUBUNIT
B: CALCIUM CHANNEL BETA-3 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)79,5532
Polymers79,5532
Non-polymers00
Water7,152397
1
A: CALCIUM CHANNEL BETA-3 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)39,7761
Polymers39,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALCIUM CHANNEL BETA-3 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)39,7761
Polymers39,7761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.300, 66.400, 90.000
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CALCIUM CHANNEL BETA-3 SUBUNIT / CAB3 / VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA-3 SUBUNIT


Mass: 39776.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54287
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE BETA SUBUNIT OF VOLTAGE-DEPENDENT CALCIUM CHANNELS CONTRIBUTES TO THE FUNCTION OF THE CALCIUM ...THE BETA SUBUNIT OF VOLTAGE-DEPENDENT CALCIUM CHANNELS CONTRIBUTES TO THE FUNCTION OF THE CALCIUM CHANNEL BY INCREASING PEAK CALCIUM CURRENT, SHIFTING THE VOLTAGE DEPENDENCIES OF ACTIVATION AND INACTIVATION.

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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 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.2
Details: HEPES PH 7.2 250 MM NACL 15% POLYETHYLENE GLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorDate: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 27894 / % possible obs: 94 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.252 / % possible all: 84

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2772 9.9 %RANDOM
Rwork0.207 ---
obs0.207 27919 93.8 %-
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å26.22 Å2
2--0.26 Å20 Å2
3----4.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4454 0 0 397 4851
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it2.692
X-RAY DIFFRACTIONc_scangle_it4.012.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.27 248 10 %
Rwork0.222 2227 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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