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- EMDB-28578: Human EMC:human Cav1.2 channel complex (Segment map 01) -

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Basic information

Entry
Database: EMDB / ID: EMD-28578
TitleHuman EMC:human Cav1.2 channel complex (Segment map 01)
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
Keywordsendoplasmic reticulum membrane protein complex / voltage-gated calcium channel / holdase / biogenesis / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen Z / Mondal A / Abderemane-Ali F / 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: Nature / Year: 2023
Title: EMC chaperone-Ca structure reveals an ion channel assembly intermediate.
Authors: Zhou Chen / Abhisek Mondal / Fayal Abderemane-Ali / Seil Jang / Sangeeta Niranjan / José L Montaño / Balyn W Zaro / Daniel L Minor /
Abstract: Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function. Structural understanding of how VGIC subunits assemble and whether chaperone ...Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function. Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (Cas) are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming Ca1 or Ca2 Caα (ref. ), and the auxiliary Caβ and Caαδ subunits. Here we present cryo-electron microscopy structures of human brain and cardiac Ca1.2 bound with Caβ to a chaperone-the endoplasmic reticulum membrane protein complex (EMC)-and of the assembled Ca1.2-Caβ-Caαδ-1 channel. These structures provide a view of an EMC-client complex and define EMC sites-the transmembrane (TM) and cytoplasmic (Cyto) docks; interaction between these sites and the client channel causes partial extraction of a pore subunit and splays open the Caαδ-interaction site. The structures identify the Caαδ-binding site for gabapentinoid anti-pain and anti-anxiety drugs, show that EMC and Caαδ interactions with the channel are mutually exclusive, and indicate that EMC-to-Caαδ hand-off involves a divalent ion-dependent step and Ca1.2 element ordering. Disruption of the EMC-Ca complex compromises Ca function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a Ca assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins.
History
DepositionOct 14, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28578.png

Downloads & links

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Map

FileDownload / File: emd_28578.map.gz / Format: CCP4 / Size: 329.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 442 pix.
= 374.197 Å		0.85 Å/pix.
x 442 pix.
= 374.197 Å		0.85 Å/pix.
x 442 pix.
= 374.197 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8466 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0036
Minimum - Maximum-0.006936765 - 0.01850254
Average (Standard dev.)0.000040482857 (±0.00039480627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-1
Dimensions442442442
Spacing442442442
CellA=B=C: 374.1972 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28578_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28578_half_map_2.map
Projections & Slices
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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

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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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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 487067
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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