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- PDB-1t0j: Crystal structure of a complex between voltage-gated calcium chan... -

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Basic information

Entry
Database: PDB / ID: 1t0j
TitleCrystal structure of a complex between voltage-gated calcium channel beta2a subunit and a peptide of the alpha1c subunit
Components
  • (voltage-gated calcium channel subunit beta2a) x 2
  • Voltage-dependent L-type calcium channel alpha-1C subunit
KeywordsSIGNALING PROTEIN / SH3 domain / nucleotide kinase like domain / ion channel / calcium channel / AID
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 / chemical synaptic transmission / perikaryon / 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
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: 2 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 9, 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: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: voltage-gated calcium channel subunit beta2a
B: voltage-gated calcium channel subunit beta2a
C: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6624
Polymers42,6273
Non-polymers351
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-30 kcal/mol
Surface area15980 Å2
MethodPISA
2
A: voltage-gated calcium channel subunit beta2a

B: voltage-gated calcium channel subunit beta2a
C: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6624
Polymers42,6273
Non-polymers351
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-27 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.756, 45.330, 60.652
Angle α, β, γ (deg.)96.81, 102.46, 98.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein voltage-gated calcium channel subunit beta2a /


Mass: 14996.776 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: CACNB2A / 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: 25321.291 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: CACNB2A / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8VGC3
#3: Protein/peptide Voltage-dependent L-type calcium channel alpha-1C subunit / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle


Mass: 2308.476 Da / Num. of mol.: 1 / Fragment: Residues 428-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA1C, CACNL1A1, CCHL1A1, CACH2, CACN2 / Plasmid: modified pET27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13936
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-Cl, PEG 4000, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 24890 / Num. obs: 24890 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.49 % / Biso Wilson estimate: 21.503 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.65
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.54 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 2503 / Rsym value: 0.385 / % possible all: 96.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TOH

1toh


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.124 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.178 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24154 1266 5.2 %RANDOM
Rwork0.19971 ---
all0.20188 24890 --
obs0.20188 23297 97.28 %-
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: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20.06 Å21.97 Å2
2---1.26 Å2-0.27 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 1 138 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212410
X-RAY DIFFRACTIONr_bond_other_d0.0020.022217
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9563262
X-RAY DIFFRACTIONr_angle_other_deg0.8735162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022621
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02460
X-RAY DIFFRACTIONr_nbd_refined0.2080.2456
X-RAY DIFFRACTIONr_nbd_other0.2390.22418
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2129
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_other0.4040.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9481.51497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77322419
X-RAY DIFFRACTIONr_scbond_it2.8363913
X-RAY DIFFRACTIONr_scangle_it4.7274.5843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 94
Rwork0.237 1721
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.923-0.31970.14790.4409-0.15540.63530.0097-0.066-0.01690.00420.06420.0076-0.0063-0.0312-0.07390.056-0.0089-0.05640.0859-0.00210.0583-2.821-14.48713.262
20.1292-0.2096-0.17270.28760.36440.5810.03480.01640.0182-0.05060.0053-0.0254-0.0799-0.0359-0.04010.0656-0.0032-0.0380.09620.00790.05341.1338.674-8.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 13628 - 123
2X-RAY DIFFRACTION2BB225 - 41424 - 213

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