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- PDB-4zw2: Crystal structure of the Mouse voltage gated calcium channel beta... -

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Basic information

Entry
Database: PDB / ID: 4zw2
TitleCrystal structure of the Mouse voltage gated calcium channel beta subunit isoform 1a in complex with Alpha Interaction Domain peptide.
Components
  • Voltage-dependent L-type calcium channel subunit alpha-1S
  • Voltage-dependent L-type calcium channel subunit beta-1,Voltage-dependent L-type calcium channel subunit beta-1
KeywordsMETAL TRANSPORT / dihydropyridine receptor / CaVbeta / excitation contraction coupling / Alpha Interacting Domain
Function / homology
Function and homology information


skeletal muscle adaptation / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / extraocular skeletal muscle development / Presynaptic depolarization and calcium channel opening / regulation of voltage-gated calcium channel activity / positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / muscle cell development / myoblast fusion ...skeletal muscle adaptation / Phase 2 - plateau phase / Phase 0 - rapid depolarisation / extraocular skeletal muscle development / Presynaptic depolarization and calcium channel opening / regulation of voltage-gated calcium channel activity / positive regulation of muscle contraction / L-type voltage-gated calcium channel complex / muscle cell development / myoblast fusion / high voltage-gated calcium channel activity / endoplasmic reticulum organization / regulation of monoatomic ion transmembrane transport / calcium ion import / I band / protein targeting to membrane / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / neuromuscular junction development / dendritic spine head / voltage-gated calcium channel complex / cellular response to caffeine / striated muscle contraction / voltage-gated calcium channel activity / skeletal muscle fiber development / skeletal muscle tissue development / T-tubule / sarcoplasmic reticulum / muscle contraction / skeletal system development / calcium ion transmembrane transport / phosphoprotein binding / sarcolemma / cellular response to amyloid-beta / calcium ion transport / presynapse / chemical synaptic transmission / postsynapse / calmodulin binding / protein domain specific binding / glutamatergic synapse / protein kinase binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S 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-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S 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 / Src homology 3 (SH3) domain profile. / SH3 domain / Ion transport domain / Ion transport protein / 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
TRIETHYLENE GLYCOL / Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent L-type calcium channel subunit beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsNorris, N.C. / Oakley, A.J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural and biophysical analyses of the skeletal dihydropyridine receptor beta subunit beta 1a reveal critical roles of domain interactions for stability.
Authors: Norris, N.C. / Joseph, S. / Aditya, S. / Karunasekara, Y. / Board, P.G. / Dulhunty, A.F. / Oakley, A.J. / Casarotto, M.G.
History
DepositionMay 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Aug 2, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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-1,Voltage-dependent L-type calcium channel subunit beta-1
B: Voltage-dependent L-type calcium channel subunit alpha-1S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0734
Polymers39,7722
Non-polymers3002
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-10 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.240, 69.371, 131.104
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-1,Voltage-dependent L-type calcium channel subunit beta-1 / CAB1 / Calcium channel voltage-dependent subunit beta 1


Mass: 37564.035 Da / Num. of mol.: 1 / Fragment: UNP residue 68-185, linker, 261-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cacnb1, Cacnlb1 / Plasmid: pHUE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8R3Z5
#2: Protein/peptide Voltage-dependent L-type calcium channel subunit alpha-1S / Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated ...Calcium channel / L type / alpha-1 polypeptide / isoform 3 / skeletal muscle / Voltage-gated calcium channel subunit alpha Cav1.1


Mass: 2208.408 Da / Num. of mol.: 1 / Fragment: UNP residues 357-374 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q02789
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.64 Å3/Da / Density % sol: 53.47 % / Description: bipyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, 0.2 M sodium acetate, 0.1 M bis-tris propane pH 8.0
PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 25, 2013
RadiationMonochromator: Varimax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 36235 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 35.45
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 4.95 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1t0j

1t0j


Resolution: 1.86→22.81 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.089 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1801 5 %RANDOM
Rwork0.16865 ---
obs0.17054 34373 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.86→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2640 0 17 285 2942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192791
X-RAY DIFFRACTIONr_bond_other_d0.0010.022706
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9743798
X-RAY DIFFRACTIONr_angle_other_deg0.93436243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88723.952124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70815492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361521
X-RAY DIFFRACTIONr_chiral_restr0.1210.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it2.9072.8641373
X-RAY DIFFRACTIONr_mcbond_other2.9062.8651374
X-RAY DIFFRACTIONr_mcangle_it3.6354.2761719
X-RAY DIFFRACTIONr_mcangle_other3.6314.2761719
X-RAY DIFFRACTIONr_scbond_it4.0653.21418
X-RAY DIFFRACTIONr_scbond_other4.0523.21418
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6954.6452068
X-RAY DIFFRACTIONr_long_range_B_refined7.55624.123366
X-RAY DIFFRACTIONr_long_range_B_other7.48923.3093228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 108 -
Rwork0.228 2447 -
obs--97.71 %
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)
10.5918-0.3231-0.40090.81980.74211.4540.00220.0639-0.0073-0.09070.0208-0.10720.09310.106-0.02290.06520.00160.01680.03830.00930.034411.001283.544513.7062
26.8333-1.38051.80025.0561-0.12786.1785-0.0109-0.20010.2830.195-0.01790.1821-0.058-0.25330.02870.0492-0.00750.03130.0149-0.01330.0356-5.8431104.341431.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 333
2X-RAY DIFFRACTION2B0 - 19

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