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- PDB-6keb: Structure basis for Diltiazem block of a voltage-gated calcium channel -

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Basic information

Entry
Database: PDB / ID: 6keb
TitleStructure basis for Diltiazem block of a voltage-gated calcium channel
ComponentsIon transport protein
KeywordsTRANSPORT PROTEIN / Tetrameric / Voltage-gated Ion Channel / Voltage-gated Calcium Channel Block / MEMBRANE PROTEIN
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / metal ion binding / identical protein binding
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Chem-D6C / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTang, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL112808 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01NS015751 United States
Howard Hughes Medical Institute United States
CitationJournal: Mol.Pharmacol. / Year: 2019
Title: Structural Basis for Diltiazem Block of a Voltage-Gated Ca2+Channel.
Authors: Tang, L. / Gamal El-Din, T.M. / Lenaeus, M.J. / Zheng, N. / Catterall, W.A.
History
DepositionJul 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,56519
Polymers131,9234
Non-polymers8,64215
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18790 Å2
ΔGint-150 kcal/mol
Surface area45380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.600, 125.630, 191.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Ion transport protein / CavAb


Mass: 32980.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C36H73NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-D6C / [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate


Mass: 414.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O4S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 5.74 Å3/Da / Density % sol: 78.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.528
11K, H, -L20.472
ReflectionResolution: 3.2→30 Å / Num. obs: 45703 / % possible obs: 90.5 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6686 / CC1/2: 0.813 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.85 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.836 / SU B: 12.206 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 2296 5 %RANDOM
Rwork0.2435 ---
obs0.2452 43340 89.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 245.66 Å2 / Biso mean: 84.033 Å2 / Biso min: 21.06 Å2
Baniso -1Baniso -2Baniso -3
1-26.62 Å20 Å20 Å2
2---1.81 Å2-0 Å2
3----24.82 Å2
Refinement stepCycle: final / Resolution: 3.2→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7269 0 195 5 7469
Biso mean--78.39 100.98 -
Num. residues----885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027656
X-RAY DIFFRACTIONr_bond_other_d0.0060.027580
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.97310407
X-RAY DIFFRACTIONr_angle_other_deg1.201317306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62521.864295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.909151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6641540
X-RAY DIFFRACTIONr_chiral_restr0.0990.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028085
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021881
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_it6.4168.5793536
X-RAY DIFFRACTIONr_mcbond_other6.48.5783535
X-RAY DIFFRACTIONr_mcangle_it9.30812.8444413
X-RAY DIFFRACTIONr_mcangle_other9.30912.8464414
X-RAY DIFFRACTIONr_scbond_it5.9248.4824120
X-RAY DIFFRACTIONr_scbond_other5.9238.4824121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.38512.6675995
X-RAY DIFFRACTIONr_long_range_B_refined12.01531113
X-RAY DIFFRACTIONr_long_range_B_other12.01531114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.281 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.613 160 -
Rwork0.441 3148 -
obs--89.41 %

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