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- EMDB-29006: human EMC:human Cav1.2 channel complex in GDN detergent at 3.1 An... -

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Basic information

Entry
Database: EMDB / ID: EMD-29006
Titlehuman EMC:human Cav1.2 channel complex in GDN detergent at 3.1 Angstrom
Map data
Sample
  • Complex: Ternary complex of the human ER membrane protein complex (EMC) with human CaV alpha1C and rabbit CaV beta3
    • Complex: Human CaV alpha1C
    • Complex: ER membrane protein complex subunit 1
    • Complex: Rabbit CaV beta3
Keywordsendoplasmic reticulum membrane protein complex / voltage-gated calcium channel / holdase / biogenesis / MEMBRANE PROTEIN
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 2, 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_29006.png

Downloads & links

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Map

FileDownload / File: emd_29006.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å		0.84 Å/pix.
x 440 pix.
= 367.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0033
Minimum - Maximum-0.0063979654 - 0.01777149
Average (Standard dev.)0.000027882807 (±0.0004968268)
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_29006_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_29006_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 the human ER membrane protein complex (EMC) wi...

EntireName: Ternary complex of the human ER membrane protein complex (EMC) with human CaV alpha1C and rabbit CaV beta3
Components
  • Complex: Ternary complex of the human ER membrane protein complex (EMC) with human CaV alpha1C and rabbit CaV beta3
    • Complex: Human CaV alpha1C
    • Complex: ER membrane protein complex subunit 1
    • Complex: Rabbit CaV beta3

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Supramolecule #1: Ternary complex of the human ER membrane protein complex (EMC) wi...

SupramoleculeName: Ternary complex of the human ER membrane protein complex (EMC) with human CaV alpha1C and rabbit CaV beta3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
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: #9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 187 KDa

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Supramolecule #3: ER membrane protein complex subunit 1

SupramoleculeName: ER membrane protein complex subunit 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 112 KDa

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Supramolecule #4: Rabbit CaV beta3

SupramoleculeName: Rabbit CaV beta3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #10
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

Concentration1.7 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:

6ww7


Details: 6WW7 (PDB ID) and 7MIY (PDB ID) used to generate the startup model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 383185
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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