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- PDB-1vyv: beta4 subunit of Ca2+ channel -

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Basic information

Entry
Database: PDB / ID: 1vyv
Titlebeta4 subunit of Ca2+ channel
ComponentsCALCIUM CHANNEL BETA-4SUBUNIT
KeywordsTRANSPORT PROTEIN / ION TRANSPORT-COMPLEX / CALCIUM CHANNEL BETA SUBUNIT / AID DOAMIN / ION TRANSPORT / IONIC CHANNEL / VOLTAGE-GATED CHANNEL / SH3 DOMAIN
Function / homology
Function and homology information


voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / high voltage-gated calcium channel activity / cAMP metabolic process / Peyer's patch development / muscle cell development / gamma-aminobutyric acid signaling pathway ...voltage-gated calcium channel activity involved in regulation of presynaptic cytosolic calcium levels / positive regulation of protein localization to nucleolus / Presynaptic depolarization and calcium channel opening / gamma-aminobutyric acid secretion / detection of light stimulus involved in visual perception / high voltage-gated calcium channel activity / cAMP metabolic process / Peyer's patch development / muscle cell development / gamma-aminobutyric acid signaling pathway / adult walking behavior / neuronal action potential propagation / nervous system process / voltage-gated calcium channel complex / neuromuscular junction development / regulation of synaptic vesicle exocytosis / negative regulation of G1/S transition of mitotic cell cycle / voltage-gated calcium channel activity / spleen development / thymus development / cellular response to leukemia inhibitory factor / synaptic transmission, glutamatergic / regulation of membrane potential / intracellular calcium ion homeostasis / calcium ion transport / presynapse / T cell receptor signaling pathway / chemical synaptic transmission / nuclear speck / negative regulation of cell population proliferation / glutamatergic synapse / protein kinase binding / plasma membrane
Similarity search - Function
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. ...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-4
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM CHANNEL BETA-4SUBUNIT
B: CALCIUM CHANNEL BETA-4SUBUNIT


Theoretical massNumber of molelcules
Total (without water)80,7522
Polymers80,7522
Non-polymers00
Water00
1
A: CALCIUM CHANNEL BETA-4SUBUNIT


Theoretical massNumber of molelcules
Total (without water)40,3761
Polymers40,3761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALCIUM CHANNEL BETA-4SUBUNIT


Theoretical massNumber of molelcules
Total (without water)40,3761
Polymers40,3761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.300, 83.200, 72.300
Angle α, β, γ (deg.)90.00, 94.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CALCIUM CHANNEL BETA-4SUBUNIT


Mass: 40376.082 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: D4A055*PLUS
Sequence detailsGENBANK CONTAINS A NON TRANSLATED DNA SEQUENCE FOR THIS ENTRY HENCE THE SEQUENCE WAS MAPPED TO ITSELF.

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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: 2.9 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.2 / Details: 20 MM NA-HEPES PH 7.2, 250 MM NACL AND 5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791
DetectorDate: Feb 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 47712 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.282 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GCOMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYU

1vyu


Resolution: 3→30 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1373 10 %RANDOM
Rwork0.248 ---
obs0.248 13771 88.8 %-
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å27.29 Å2
2---4.51 Å20 Å2
3---0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 0 0 4361
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.951.5
X-RAY DIFFRACTIONc_mcangle_it52
X-RAY DIFFRACTIONc_scbond_it4.132
X-RAY DIFFRACTIONc_scangle_it7.122.5
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.391 123 9.8 %
Rwork0.371 1130 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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