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- PDB-5v2q: CaV beta2a subunit: CaV1.2 AID-CEN complex -

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Basic information

Entry
Database: PDB / ID: 5v2q
TitleCaV beta2a subunit: CaV1.2 AID-CEN complex
Components
  • Voltage-dependent L-type calcium channel subunit alpha-1C
  • Voltage-dependent L-type calcium channel subunit beta-2,Voltage-dependent L-type calcium channel subunit beta-2
KeywordsTRANSPORT PROTEIN / ion channel / signaling / calcium
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 / 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 insulin secretion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / immune system development ...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 / 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 insulin secretion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / immune system development / positive regulation of high voltage-gated calcium channel activity / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / membrane depolarization during AV node cell action potential / regulation of presynaptic cytosolic calcium ion concentration / photoreceptor ribbon synapse / positive regulation of adenylate cyclase activity / cardiac conduction / L-type voltage-gated calcium channel complex / membrane depolarization during cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / positive regulation of calcium ion transport / camera-type eye development / NCAM1 interactions / calcium ion import / embryonic forelimb morphogenesis / calcium ion transport into cytosol / cell communication by electrical coupling involved in cardiac conduction / neuromuscular junction development / voltage-gated calcium channel complex / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / alpha-actinin binding / calcium ion import across plasma membrane / calcium channel regulator activity / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / visual perception / Regulation of insulin secretion / protein localization to plasma membrane / calcium ion transmembrane transport / postsynaptic density membrane / phosphoprotein binding / Adrenaline,noradrenaline inhibits insulin secretion / Z disc / calcium ion transport / actin filament binding / presynapse / heart development / positive regulation of cytosolic calcium ion concentration / perikaryon / chemical synaptic transmission / postsynaptic density / calmodulin binding / protein domain specific binding / dendrite / protein kinase binding / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C 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-dependent calcium channel, L-type, beta-2 subunit / CACNB2, SH3 domain / Voltage-dependent calcium channel, L-type, alpha-1C 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. / SH3-like domain superfamily / Ion transport domain / Ion transport protein / 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
1,3-bis(bromomethyl)benzene / Voltage-dependent L-type calcium channel subunit alpha-1C / Voltage-dependent L-type calcium channel subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFindeisen, F. / Campiglio, M. / Jo, H. / Rumpf, C.H. / Pope, L. / Flucher, B. / Degrado, W.F. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL080050 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM54616 United States
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Stapled Voltage-Gated Calcium Channel (CaV) alpha-Interaction Domain (AID) Peptides Act As Selective Protein-Protein Interaction Inhibitors of CaV Function.
Authors: Findeisen, F. / Campiglio, M. / Jo, H. / Abderemane-Ali, F. / Rumpf, C.H. / Pope, L. / Rossen, N.D. / Flucher, B.E. / DeGrado, W.F. / Minor, D.L.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit beta-2,Voltage-dependent L-type calcium channel subunit beta-2
B: Voltage-dependent L-type calcium channel subunit alpha-1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5404
Polymers41,2412
Non-polymers2992
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-20 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.975, 61.920, 129.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Voltage-dependent L-type calcium channel subunit beta-2,Voltage-dependent L-type calcium channel subunit beta-2 / CAB2 / Calcium channel voltage-dependent subunit beta 2


Mass: 39099.562 Da / Num. of mol.: 1 / Fragment: beta2a subunit (UNP residues 68-189,203-425)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacnb2, Cacnlb2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VGC3
#2: Protein/peptide Voltage-dependent L-type calcium channel subunit alpha-1C / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium ...Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Voltage-gated calcium channel subunit alpha Cav1.2


Mass: 2141.377 Da / Num. of mol.: 1 / Fragment: AID-CEN (UNP residues 427-445) / Mutation: K427A, Q428S, Q429P, K435C, D439C / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13936
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-8VY / 1,3-bis(bromomethyl)benzene / alpha,alpha'-dibromo-m-xylene


Mass: 263.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8Br2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5-1.7 M ammonium sulfate, 5 mM BME, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 14, 2012
RadiationMonochromator: Si(111) double crystal Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.7→61.92 Å / Num. obs: 43025 / % possible obs: 87 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 0.6 / Num. unique all: 3345 / % possible all: 47.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLM7.0.4data reduction
SCALA3.3.20data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1T3S

1t3s


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2178 5.1 %RANDOM
Rwork0.154 ---
obs0.156 40696 86.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 9 457 2946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192596
X-RAY DIFFRACTIONr_bond_other_d00.022542
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9693524
X-RAY DIFFRACTIONr_angle_other_deg4.3493.0015856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73624.454119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0215459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4361518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212910
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02574
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5262.2271273
X-RAY DIFFRACTIONr_mcbond_other2.5212.2251272
X-RAY DIFFRACTIONr_mcangle_it3.7153.3071586
X-RAY DIFFRACTIONr_mcangle_other3.7153.3081587
X-RAY DIFFRACTIONr_scbond_it4.0342.6461323
X-RAY DIFFRACTIONr_scbond_other4.0332.6461324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4073.771933
X-RAY DIFFRACTIONr_long_range_B_refined9.43720.2023273
X-RAY DIFFRACTIONr_long_range_B_other9.05718.7853033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 75 -
Rwork0.353 1411 -
obs--41.84 %

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