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- EMDB-29015: Structure of the human L-type voltage-gated calcium channel Cav1.... -

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Basic information

Entry
Database: EMDB / ID: EMD-29015
TitleStructure of the human L-type voltage-gated calcium channel Cav1.2 complexed with gabapentin (consensus map)
Map data
Sample
  • Cell: Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-1 and rabbit CaV beta3
    • Complex: Human CaV alpha1C
    • Complex: Rabbit CaV alpha2delta-1
    • Complex: Rabbit CaV beta3
Keywordsvoltage-gated calcium channel / CaV alpha2delta / drug binding / gabapentin / MEMBRANE PROTEIN / gbp
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen Z / Mondal A / Minor DL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL080050 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC007664 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structural basis for Caαδ:gabapentin binding.
Authors: Zhou Chen / Abhisek Mondal / Daniel L Minor /
Abstract: Gabapentinoid drugs for pain and anxiety act on the Caαδ-1 and Caαδ-2 subunits of high-voltage-activated calcium channels (Ca1s and Ca2s). Here we present the cryo-EM structure of the gabapentin- ...Gabapentinoid drugs for pain and anxiety act on the Caαδ-1 and Caαδ-2 subunits of high-voltage-activated calcium channels (Ca1s and Ca2s). Here we present the cryo-EM structure of the gabapentin-bound brain and cardiac Ca1.2/Caβ/Caαδ-1 channel. The data reveal a binding pocket in the Caαδ-1 dCache1 domain that completely encapsulates gabapentin and define Caαδ isoform sequence variations that explain the gabapentin binding selectivity of Caαδ-1 and Caαδ-2.
History
DepositionDec 5, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJul 5, 2023-
Current statusJul 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29015.png

Downloads & links

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Map

FileDownload / File: emd_29015.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.0052684983 - 0.01626565
Average (Standard dev.)0.0000062914396 (±0.00038099935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 367.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29015_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29015_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-...

EntireName: Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-1 and rabbit CaV beta3
Components
  • Cell: Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-1 and rabbit CaV beta3
    • Complex: Human CaV alpha1C
    • Complex: Rabbit CaV alpha2delta-1
    • Complex: Rabbit CaV beta3

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Supramolecule #1: Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-...

SupramoleculeName: Ternary complex of human CaV alpha1C with rabbit CaV alpha2delta-1 and rabbit CaV beta3
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human CaV alpha1C

SupramoleculeName: Human CaV alpha1C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 187 KDa

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Supramolecule #3: Rabbit CaV alpha2delta-1

SupramoleculeName: Rabbit CaV alpha2delta-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 125 KDa

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Supramolecule #4: Rabbit CaV beta3

SupramoleculeName: Rabbit CaV beta3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 100 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8eog

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 259107
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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