8EOI

Structure of a human EMC:human Cav1.2 channel complex in GDN detergent


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

EMC chaperone-Ca V structure reveals an ion channel assembly intermediate.

Chen, Z.Mondal, A.Abderemane-Ali, F.Jang, S.Niranjan, S.Montano, J.L.Zaro, B.W.Minor Jr., D.L.

(2023) Nature 619: 410-419

  • DOI: https://doi.org/10.1038/s41586-023-06175-5
  • Primary Citation of Related Structures:  
    8EOG, 8EOI

  • PubMed Abstract: 

    Voltage-gated ion channels (VGICs) comprise multiple structural units, the assembly of which is required for function 1,2 . Structural understanding of how VGIC subunits assemble and whether chaperone proteins are required is lacking. High-voltage-activated calcium channels (Ca V s) 3,4 are paradigmatic multisubunit VGICs whose function and trafficking are powerfully shaped by interactions between pore-forming Ca V 1 or Ca V 2 Ca V α 1 (ref. 3 ), and the auxiliary Ca V β 5 and Ca V α 2 δ subunits 6,7 . Here we present cryo-electron microscopy structures of human brain and cardiac Ca V 1.2 bound with Ca V β 3 to a chaperone-the endoplasmic reticulum membrane protein complex (EMC) 8,9 -and of the assembled Ca V 1.2-Ca V β 3 -Ca V α 2 δ-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 Ca V α 2 δ-interaction site. The structures identify the Ca V α 2 δ-binding site for gabapentinoid anti-pain and anti-anxiety drugs 6 , show that EMC and Ca V α 2 δ interactions with the channel are mutually exclusive, and indicate that EMC-to-Ca V α 2 δ hand-off involves a divalent ion-dependent step and Ca V 1.2 element ordering. Disruption of the EMC-Ca V complex compromises Ca V function, suggesting that the EMC functions as a channel holdase that facilitates channel assembly. Together, the structures reveal a Ca V assembly intermediate and EMC client-binding sites that could have wide-ranging implications for the biogenesis of VGICs and other membrane proteins.


  • Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1973Homo sapiensMutation(s): 0 
Gene Names: EMC1KIAA0090PSEC0263
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N766 (Homo sapiens)
Explore Q8N766 
Go to UniProtKB:  Q8N766
PHAROS:  Q8N766
GTEx:  ENSG00000127463 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N766
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2291Homo sapiensMutation(s): 0 
Gene Names: EMC2KIAA0103TTC35
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15006 (Homo sapiens)
Explore Q15006 
Go to UniProtKB:  Q15006
PHAROS:  Q15006
GTEx:  ENSG00000104412 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15006
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3258Homo sapiensMutation(s): 0 
Gene Names: EMC3TMEM111
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0I2 (Homo sapiens)
Explore Q9P0I2 
Go to UniProtKB:  Q9P0I2
PHAROS:  Q9P0I2
GTEx:  ENSG00000125037 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P0I2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5D [auth E]101Homo sapiensMutation(s): 0 
Gene Names: MMGT1EMC5TMEM32
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4V1 (Homo sapiens)
Explore Q8N4V1 
Go to UniProtKB:  Q8N4V1
PHAROS:  Q8N4V1
GTEx:  ENSG00000169446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N4V1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6E [auth F]100Homo sapiensMutation(s): 0 
Gene Names: EMC6TMEM93
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV81 (Homo sapiens)
Explore Q9BV81 
Go to UniProtKB:  Q9BV81
PHAROS:  Q9BV81
GTEx:  ENSG00000127774 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BV81
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 7F [auth G]116Homo sapiensMutation(s): 0 
Gene Names: EMC7C11orf3C15orf24HT022UNQ905/PRO1926
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPA0 (Homo sapiens)
Explore Q9NPA0 
Go to UniProtKB:  Q9NPA0
PHAROS:  Q9NPA0
GTEx:  ENSG00000134153 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPA0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 8G [auth H]208Homo sapiensMutation(s): 0 
Gene Names: EMC8C16orf2C16orf4COX4ALCOX4NBFAM158BNOC4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O43402 (Homo sapiens)
Explore O43402 
Go to UniProtKB:  O43402
PHAROS:  O43402
GTEx:  ENSG00000131148 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43402
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 10H [auth I]157Homo sapiensMutation(s): 0 
Gene Names: EMC10C19orf63INM02UNQ764/PRO1556
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5UCC4 (Homo sapiens)
Explore Q5UCC4 
Go to UniProtKB:  Q5UCC4
PHAROS:  Q5UCC4
GTEx:  ENSG00000161671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UCC4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1CI [auth K]1,550Homo sapiensMutation(s): 0 
Gene Names: CACNA1CCACH2CACN2CACNL1A1CCHL1A1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13936 (Homo sapiens)
Explore Q13936 
Go to UniProtKB:  Q13936
PHAROS:  Q13936
GTEx:  ENSG00000151067 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13936
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-3324Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNB3CACNLB3
UniProt
Find proteins for P54286 (Oryctolagus cuniculus)
Explore P54286 
Go to UniProtKB:  P54286
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54286
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 4K [auth D]170Homo sapiensMutation(s): 0 
Gene Names: EMC4TMEM85HSPC184PIG17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5J8M3 (Homo sapiens)
Explore Q5J8M3 
Go to UniProtKB:  Q5J8M3
PHAROS:  Q5J8M3
GTEx:  ENSG00000128463 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5J8M3
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, M, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9Z9
Query on 9Z9

Download Ideal Coordinates CCD File 
P [auth K](3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
C34 H56 O5
CEEBZAXXSRFQIC-GZSGZGDASA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL080050
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesDC007664

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references