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- PDB-6jp5: Rabbit Cav1.1-Nifedipine Complex -

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Basic information

Entry
Database: PDB / ID: 6jp5
TitleRabbit Cav1.1-Nifedipine Complex
Components
  • (Voltage-dependent L-type calcium channel subunit ...) x 2
  • (Voltage-dependent calcium channel ...Voltage-gated calcium channel) x 2
KeywordsMEMBRANE PROTEIN / Membrane protein complex modulated by FDA approved drug.
Function / homology
Function and homology information


L-type voltage-gated calcium channel complex / sarcoplasmic reticulum calcium ion transport / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium ion import across plasma membrane / calcium channel regulator activity / voltage-gated ion channel activity / cellular response to caffeine / voltage-gated calcium channel activity / regulation of ion transmembrane transport / T-tubule ...L-type voltage-gated calcium channel complex / sarcoplasmic reticulum calcium ion transport / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / calcium ion import across plasma membrane / calcium channel regulator activity / voltage-gated ion channel activity / cellular response to caffeine / voltage-gated calcium channel activity / regulation of ion transmembrane transport / T-tubule / regulation of ryanodine-sensitive calcium-release channel activity / calcium channel activity / calcium ion transmembrane transport / sarcolemma / ion channel binding / calmodulin binding / integral component of plasma membrane / metal ion binding
Ion transport domain / Guanylate kinase/L-type calcium channel beta subunit / PMP-22/EMP/MP20/Claudin superfamily / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / von Willebrand factor type A domain / Voltage-dependent calcium channel, gamma subunit / von Willebrand factor, type A ...Ion transport domain / Guanylate kinase/L-type calcium channel beta subunit / PMP-22/EMP/MP20/Claudin superfamily / Voltage-dependent calcium channel, gamma-1 subunit / Voltage-dependent calcium channel, L-type, beta-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, L-type, alpha-1S subunit / von Willebrand factor type A domain / Voltage-dependent calcium channel, gamma subunit / von Willebrand factor, type A / VWA N-terminal / Voltage-dependent calcium channel, alpha-2/delta subunit, conserved region / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage-dependent channel domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-dependent calcium channel, alpha-1 subunit / SH3 domain / von Willebrand factor A-like domain superfamily / Voltage gated calcium channel IQ domain / VWFA domain profile. / Src homology 3 (SH3) domain profile. / Voltage-dependent L-type calcium channel, IQ-associated / Voltage-gated calcium channel subunit alpha, C-term / PMP-22/EMP/MP20/Claudin tight junction / Voltage gated calcium channel subunit beta domain 4Aa N terminal / Neuronal voltage-dependent calcium channel alpha 2acd / Voltage-dependent calcium channel, L-type, beta subunit / VWA N-terminal / Guanylate kinase / Ion transport protein / SH3-like domain superfamily
Voltage-dependent L-type calcium channel subunit alpha-1S / Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-dependent L-type calcium channel subunit beta-1 / Voltage-dependent calcium channel gamma-1 subunit
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhao, Y. / Huang, G. / Wu, J. / Yan, N.
Funding supportChina , 6件
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500402China
Ministry of Science and Technology (China)2015CB910101China
National Natural Science Foundation of China31621092China
National Natural Science Foundation of China31630017China
National Institutes of Health/National Institute of General Medical SciencesR01GM130762China
National Natural Science Foundation of China81861138009China
CitationJournal: To Be Published
Title: Molecular basis for the modulation of L-type voltage-gated Ca2+ channels by antagonistic and agonistic compounds
Authors: Zhao, Y. / Huang, G. / Wu, J. / Yan, N.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 25, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
A: Voltage-dependent L-type calcium channel subunit alpha-1S
E: Voltage-dependent calcium channel gamma-1 subunit
F: Voltage-dependent calcium channel subunit alpha-2/delta-1
B: Voltage-dependent L-type calcium channel subunit beta-1
C: Voltage-dependent L-type calcium channel subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,03444
Polymers458,2845
Non-polymers12,75039
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: scanning transmission electron microscopy
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25100 Å2
ΔGint-87 kcal/mol
Surface area130810 Å2
MethodPISA

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Components

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Voltage-dependent L-type calcium channel subunit ... , 2 types, 3 molecules ABC

#1: 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 subunit alpha Cav1.1


Mass: 212240.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P07293
#4: Protein/peptide Voltage-dependent L-type calcium channel subunit beta-1 / CAB1 / Calcium channel voltage-dependent subunit beta 1


Mass: 49642.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNB1, CACNLB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19517

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Voltage-dependent calcium channel ... , 2 types, 2 molecules EF

#2: Protein/peptide Voltage-dependent calcium channel gamma-1 subunit / Dihydropyridine-sensitive L-type / skeletal muscle calcium channel subunit gamma


Mass: 25082.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P19518
#3: Protein/peptide Voltage-dependent calcium channel subunit alpha-2/delta-1 / Voltage-gated calcium channel / Voltage-gated calcium channel subunit alpha-2/delta-1


Mass: 121675.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13806

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Non-polymers , 7 types, 39 molecules

#5: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 23
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Calcium
#7: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid *YM
#8: Chemical ChemComp-C5U / dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate


Mass: 346.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N2O6
#9: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid *YM
#10: Chemical ChemComp-ETA / ETHANOLAMINE


Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO / Ethanolamine
#11: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Mannose

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Details

Sequence detailsAs for the unusual connection between Y619-S621 of Chain F, the original amino acid for S620 is ...As for the unusual connection between Y619-S621 of Chain F, the original amino acid for S620 is Y620 and the density for this large side chain is missing from reconstruction. Authors suspect this to be a result of alternative splicing. The density in this beta strand, Y619 and S621, is very clear and allows accurate side chain assignment for this area and surrounding areas.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Cav1.1-drug complex1,2,3,40MULTIPLE SOURCES
2Cav1.1-beta1a-alpha2-delta1-gamma complex2, 3, 41NATURAL
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 245171 / Symmetry type: POINT

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