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- EMDB-9868: Rabbit Cav1.1-Verapamil Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9868
TitleRabbit Cav1.1-Verapamil Complex
Map data
SampleCav1.1-drug complex
  • Cav1.1-beta1a-alpha2-delta1-gamma complex
  • Voltage-dependent L-type calcium channel subunit alpha-1S
  • (Voltage-dependent calcium channel ...Voltage-gated calcium channel) x 2
  • (Voltage-dependent L-type calcium channel subunit beta- ...) x 2
  • (ligand) x 8
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) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhao Y / Huang G / Wu J / Yan N
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 ReportPDB-ID: 6jpa

SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2019 / Header (metadata) release: May 1, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jpa
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9868.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 349.12 Å
1.09 Å/pix.
x 320 pix.
= 349.12 Å
1.09 Å/pix.
x 320 pix.
= 349.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.14246978 - 0.26829797
Average (Standard dev.)0.00007790376 (±0.0051421314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1420.2680.000

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Supplemental data

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Sample components

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Entire Cav1.1-drug complex

EntireName: Cav1.1-drug complex / Number of components: 15

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Component #1: protein, Cav1.1-drug complex

ProteinName: Cav1.1-drug complex / Recombinant expression: No

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Component #2: protein, Cav1.1-beta1a-alpha2-delta1-gamma complex

ProteinName: Cav1.1-beta1a-alpha2-delta1-gamma complex / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #3: protein, Voltage-dependent L-type calcium channel subunit alpha-1S

ProteinName: Voltage-dependent L-type calcium channel subunit alpha-1S
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 172.146531 kDa
SourceSpecies: Rabbit (rabbit)

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Component #4: protein, Voltage-dependent calcium channel gamma-1 subunit

ProteinName: Voltage-dependent calcium channel gamma-1 subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.082254 kDa
SourceSpecies: Rabbit (rabbit)

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Component #5: protein, Voltage-dependent L-type calcium channel subunit beta-1

ProteinName: Voltage-dependent L-type calcium channel subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.64243 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Voltage-dependent L-type calcium channel subunit beta-1

ProteinName: Voltage-dependent L-type calcium channel subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.898285 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: protein, Voltage-dependent calcium channel subunit alpha-2/delta-1

ProteinName: Voltage-dependent calcium channel subunit alpha-2/delta-1Voltage-gated calcium channel
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 118.641398 kDa
SourceSpecies: Rabbit (rabbit)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 23 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #9: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Component #10: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Component #11: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

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Component #12: ligand, (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)b...

LigandName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.544805 kDa

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Component #13: ligand, (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)e...

LigandName: (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.454602 kDa

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Component #14: ligand, ETHANOLAMINE

LigandName: ETHANOLAMINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.108305 MDa

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Component #15: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 433477
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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