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- PDB-1vyt: beta3 subunit complexed with aid -

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Basic information

Entry
Database: PDB / ID: 1vyt
Titlebeta3 subunit complexed with aid
Components
  • CALCIUM CHANNEL BETA-3 SUBUNIT
  • VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT
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


cell communication involved in cardiac conduction / negative regulation of detection of mechanical stimulus involved in sensory perception of touch / caveolar macromolecular signaling complex / positive regulation of membrane depolarization / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / positive regulation of high voltage-gated calcium channel activity / growth hormone secretion / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential ...cell communication involved in cardiac conduction / negative regulation of detection of mechanical stimulus involved in sensory perception of touch / caveolar macromolecular signaling complex / positive regulation of membrane depolarization / Phase 0 - rapid depolarisation / Phase 2 - plateau phase / positive regulation of high voltage-gated calcium channel activity / growth hormone secretion / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / regulation of membrane hyperpolarization / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / immune system development / Regulation of insulin secretion / positive regulation of adenylate cyclase activity / regulation of membrane repolarization during action potential / Presynaptic depolarization and calcium channel opening / membrane depolarization during atrial cardiac muscle cell action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / high voltage-gated calcium channel activity / membrane depolarization during AV node cell action potential / corpus callosum development / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / calcium-ion regulated exocytosis / smooth muscle contraction involved in micturition / regulation of ventricular cardiac muscle cell action potential / regulation of organ growth / optic nerve development / camera-type eye development / cardiac muscle cell action potential involved in contraction / embryonic forelimb morphogenesis / calcium ion import / calcium ion transport into cytosol / response to alcohol / adult walking behavior / insulin secretion / voltage-gated calcium channel complex / axon development / exocytosis / alpha-actinin binding / regulation of heart rate by cardiac conduction / calcium ion import across plasma membrane / smooth muscle contraction / positive regulation of protein targeting to membrane / positive regulation of excitatory postsynaptic potential / detection of mechanical stimulus involved in sensory perception of pain / regulation of vasoconstriction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated calcium channel activity / translation initiation factor binding / T-tubule / protein phosphatase 2A binding / dendritic shaft / protein localization to plasma membrane / calcium channel regulator activity / response to nutrient levels / establishment of localization in cell / postsynaptic density membrane / positive regulation of insulin secretion / sarcolemma / cerebral cortex development / visual learning / calcium ion transmembrane transport / regulation of blood pressure / Z disc / cellular response to amyloid-beta / intracellular calcium ion homeostasis / calcium ion transport / glucose homeostasis / T cell receptor signaling pathway / heart development / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / perikaryon / cellular response to hypoxia / chemical synaptic transmission / transmembrane transporter binding / postsynaptic membrane / calmodulin binding / postsynaptic density / apical plasma membrane / protein domain specific binding / axon / neuronal cell body / synapse / dendrite / protein kinase binding / glutamatergic synapse / enzyme binding / cell surface / protein-containing complex / metal ion binding / membrane / plasma 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 calcium channel, L-type, alpha-1C subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / 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-dependent calcium channel, L-type, beta-3 subunit / Voltage-dependent L-type calcium channel subunit beta-3, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-dependent calcium channel, L-type, beta subunit / Voltage-dependent L-type calcium channel subunit beta-1-4, N-terminal A domain / 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. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ion transport domain / Ion transport protein / Roll / P-loop containing nucleotide triphosphate hydrolases / 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-1C / Voltage-dependent L-type calcium channel subunit beta-3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, Y.-H. / Li, M.-H. / Zhang, Y. / He, L.-L. / Yamada, Y. / Fitzmaurice, A. / Yang, S. / Zhang, H. / Tong, L. / 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM CHANNEL BETA-3 SUBUNIT
B: CALCIUM CHANNEL BETA-3 SUBUNIT
E: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT
F: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)85,1534
Polymers85,1534
Non-polymers00
Water1,38777
1
A: CALCIUM CHANNEL BETA-3 SUBUNIT
E: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)42,5762
Polymers42,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CALCIUM CHANNEL BETA-3 SUBUNIT
F: VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT


Theoretical massNumber of molelcules
Total (without water)42,5762
Polymers42,5762
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)252.300, 69.000, 60.700
Angle α, β, γ (deg.)90.00, 96.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsAN INTERMOLECULAR DISULFIDE LINKAGE (A71CYS - B71CYS) ISLIKELY FORMED IN THE CRYSTAL PACKING DURING THECRYSTALLIZATION EXPERIMENT

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Components

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


Mass: 39494.891 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: Protein/peptide VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA-1C SUBUNIT / CALCIUM CHANNEL L TYPE ALPHA-1 POLYPEPTIDE ISOFORM 1 FROM CARDIAC MUSCLE / RAT BRAIN CLASS C


Mass: 3081.388 Da / Num. of mol.: 2 / Fragment: RESIDUES 452-476
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: P22002
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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.
Has protein modificationY

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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: 44 %
Crystal growpH: 8 / Details: TRIS-HCL PH 8.0, 150 MM MGCL2, 15 PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9202
DetectorDate: Mar 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 32147 / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.319 / % possible all: 77

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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: 2.6→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.272 --
Rwork0.231 --
obs0.231 32147 96 %
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 0 77 4962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10 / % reflection obs: 77 %

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