6WB9

Structure of the S. cerevisiae ER membrane complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the ER membrane complex, a transmembrane-domain insertase.

Bai, L.You, Q.Feng, X.Kovach, A.Li, H.

(2020) Nature 584: 475-478

  • DOI: https://doi.org/10.1038/s41586-020-2389-3
  • Primary Citation of Related Structures:  
    6WB9

  • PubMed Abstract: 

    The endoplasmic reticulum (ER) membrane complex (EMC) cooperates with the Sec61 translocon to co-translationally insert a transmembrane helix (TMH) of many multi-pass integral membrane proteins into the ER membrane, and it is also responsible for inserting the TMH of some tail-anchored proteins 1-3 . How EMC accomplishes this feat has been unclear. Here we report the first, to our knowledge, cryo-electron microscopy structure of the eukaryotic EMC. We found that the Saccharomyces cerevisiae EMC contains eight subunits (Emc1-6, Emc7 and Emc10), has a large lumenal region and a smaller cytosolic region, and has a transmembrane region formed by Emc4, Emc5 and Emc6 plus the transmembrane domains of Emc1 and Emc3. We identified a five-TMH fold centred around Emc3 that resembles the prokaryotic YidC insertase and that delineates a largely hydrophilic client protein pocket. The transmembrane domain of Emc4 tilts away from the main transmembrane region of EMC and is partially mobile. Mutational studies demonstrated that the flexibility of Emc4 and the hydrophilicity of the client pocket are required for EMC function. The EMC structure reveals notable evolutionary conservation with the prokaryotic insertases 4,5 , suggests that eukaryotic TMH insertion involves a similar mechanism, and provides a framework for detailed understanding of membrane insertion for numerous eukaryotic integral membrane proteins and tail-anchored proteins.


  • Organizational Affiliation

    Structural Biology Program, Van Andel Institute, Grand Rapids, MI, USA. lin.bai@vai.org.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum membrane protein complex subunit 10A [auth 0]205Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q12025 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12025
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UniProt GroupQ12025
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1B [auth 1]760Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P25574 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP25574
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2C [auth 2]292Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P47133 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP47133
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3D [auth 3]253Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP36039
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 4E [auth 4]190Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53073
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5F [auth 5]141Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P40540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6G [auth 6]108Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q12431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOP4H [auth 7]234Saccharomyces cerevisiae W303Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P39543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
L [auth 4],
M [auth 5]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth 1]
J [auth 1]
K [auth 1]
N [auth 7]
O [auth 7]
I [auth 1],
J [auth 1],
K [auth 1],
N [auth 7],
O [auth 7],
P [auth 7]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONCoot
RECONSTRUCTIONUCSF Chimera

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2020-06-03 
  • Deposition Author(s): Bai, L., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA231466

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-17
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2020-09-02
    Changes: Database references, Structure summary