6WW7

Structure of the human ER membrane protein complex in a lipid nanodisc


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 2.1 of the entry. See complete history


Literature

Structural basis for membrane insertion by the human ER membrane protein complex.

Pleiner, T.Tomaleri, G.P.Januszyk, K.Inglis, A.J.Hazu, M.Voorhees, R.M.

(2020) Science 369: 433-436

  • DOI: https://doi.org/10.1126/science.abb5008
  • Primary Citation of Related Structures:  
    6WW7

  • PubMed Abstract: 

    A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved co- and posttranslational insertase at the ER. We determined the structure of the human EMC in a lipid nanodisc to an overall resolution of 3.4 angstroms by cryo-electron microscopy, permitting building of a nearly complete atomic model. We used structure-guided mutagenesis to demonstrate that substrate insertion requires a methionine-rich cytosolic loop and occurs via an enclosed hydrophilic vestibule within the membrane formed by the subunits EMC3 and EMC6. We propose that the EMC uses local membrane thinning and a positively charged patch to decrease the energetic barrier for insertion into the bilayer.


  • Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1993Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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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 
Membrane Entity: Yes 
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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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PHAROS:  Q9P0I2
GTEx:  ENSG00000125037 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ER Membrane Protein Complex Subunit 414Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane magnesium transporter 1131Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  Q8N4V1
GTEx:  ENSG00000169446 
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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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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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GTEx:  ENSG00000134153 
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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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GTEx:  ENSG00000131148 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 10262Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000161671 
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Oligosaccharides

Help

Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A],
M [auth I]
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM137412

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-06-03
    Changes: Database references
  • Version 1.2: 2020-06-10
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-05
    Changes: Database references