7KRA

Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to Fab-DH4 in lipid nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients.

Miller-Vedam, L.E.Brauning, B.Popova, K.D.Schirle Oakdale, N.T.Bonnar, J.L.Prabu, J.R.Boydston, E.A.Sevillano, N.Shurtleff, M.J.Stroud, R.M.Craik, C.S.Schulman, B.A.Frost, A.Weissman, J.S.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.62611
  • Primary Citation of Related Structures:  
    7ADO, 7ADP, 7KRA, 7KTX

  • PubMed Abstract: 

    Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.


  • Organizational Affiliation

    Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San Francisco, San Francisco, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 1760Saccharomyces cerevisiaeMutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 2292Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P47133 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 3253Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36039 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 4190Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P53073 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 5182Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P40540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ER membrane protein complex subunit 6108Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q12431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SOP4234Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P39543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum membrane protein complex subunit 10205Saccharomyces cerevisiaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q12025 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Fab DH4 heavy chain254Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Fab DH4 light chain234Homo sapiensMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned helixK [auth M],
L [auth N]
24Saccharomyces cerevisiaeMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/Office of the DirectorUnited States1DP2OD017690-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references