8J0O

cryo-EM structure of human EMC and VDAC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 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

Structural insights into human EMC and its interaction with VDAC.

Li, M.Zhang, C.Xu, Y.Li, S.Huang, C.Wu, J.Lei, M.

(2024) Aging (Albany NY) 16: 5501-5525

  • DOI: https://doi.org/10.18632/aging.205660
  • Primary Citation of Related Structures:  
    8J0N, 8J0O

  • PubMed Abstract: 

    The endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved, multi-subunit complex acting as an insertase at the ER membrane. Growing evidence shows that the EMC is also involved in stabilizing and trafficking membrane proteins. However, the structural basis and regulation of its multifunctionality remain elusive. Here, we report cryo-electron microscopy structures of human EMC in apo- and voltage-dependent anion channel (VDAC)-bound states at resolutions of 3.47 Å and 3.32 Å, respectively. We discovered a specific interaction between VDAC proteins and the EMC at mitochondria-ER contact sites, which is conserved from yeast to humans. Moreover, we identified a gating plug located inside the EMC hydrophilic vestibule, the substrate-binding pocket for client insertion. Conformation changes of this gating plug during the apo-to-VDAC-bound transition reveal that the EMC unlikely acts as an insertase in the VDAC1-bound state. Based on the data analysis, the gating plug may regulate EMC functions by modifying the hydrophilic vestibule in different states. Our discovery offers valuable insights into the structural basis of EMC's multifunctionality.


  • Organizational Affiliation

    Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1993Homo sapiensMutation(s): 0 
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Find proteins for Q8N766 (Homo sapiens)
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PHAROS:  Q8N766
GTEx:  ENSG00000127463 
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UniProt GroupQ8N766
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104412 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125037 
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UniProt GroupQ9P0I2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 4183Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000128463 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169446 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127774 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 7242Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134153 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 8210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131148 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 10I [auth J]207Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161671 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent anion-selective channel protein 1J [auth K]283Homo sapiensMutation(s): 0 
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Find proteins for P21796 (Homo sapiens)
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GTEx:  ENSG00000213585 
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Oligosaccharides

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Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth L],
L [auth M],
M [auth N]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930063

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references