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 1.2 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 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N766 (Homo sapiens)
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Go to UniProtKB:  Q8N766
PHAROS:  Q8N766
GTEx:  ENSG00000127463 
Entity Groups  
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UniProt GroupQ8N766
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q8N766-1
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2297Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q15006 (Homo sapiens)
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PHAROS:  Q15006
GTEx:  ENSG00000104412 
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UniProt GroupQ15006
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3261Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9P0I2 (Homo sapiens)
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Go to UniProtKB:  Q9P0I2
PHAROS:  Q9P0I2
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 
Membrane Entity: Yes 
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Find proteins for Q5J8M3 (Homo sapiens)
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PHAROS:  Q5J8M3
GTEx:  ENSG00000128463 
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UniProt GroupQ5J8M3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5131Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q8N4V1 (Homo sapiens)
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PHAROS:  Q8N4V1
GTEx:  ENSG00000169446 
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UniProt GroupQ8N4V1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6110Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9BV81 (Homo sapiens)
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PHAROS:  Q9BV81
GTEx:  ENSG00000127774 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 7242Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9NPA0 (Homo sapiens)
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PHAROS:  Q9NPA0
GTEx:  ENSG00000134153 
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UniProt GroupQ9NPA0
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 8210Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for O43402 (Homo sapiens)
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PHAROS:  O43402
GTEx:  ENSG00000131148 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 10I [auth J]207Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q5UCC4 (Homo sapiens)
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PHAROS:  Q5UCC4
GTEx:  ENSG00000161671 
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UniProt GroupQ5UCC4
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q5UCC4-1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Voltage-dependent anion-selective channel protein 1J [auth K]283Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P21796 (Homo sapiens)
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PHAROS:  P21796
GTEx:  ENSG00000213585 
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UniProt GroupP21796
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Oligosaccharides

Help

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
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary