- EMDB-23033: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein... -
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Basic information
Entry
Database: EMDB / ID: EMD-23033
Title
Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent
Map data
sharpened map
Sample
Complex: S. cerevisiae endoplasmic reticulum membrane protein complex (EMC) bound to Fab in DDM detergent
Complex: endoplasmic reticulum membrane protein complex
Protein or peptide: x 9 types
Complex: Fab DH4
Protein or peptide: x 2 types
Ligand: x 1 types
Function / homology
Function and homology information
EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / protein folding in endoplasmic reticulum / phospholipid transport / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / phospholipid metabolic process / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus Similarity search - Function
Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 ...Protein Sop4 / : / Suppressor of PMA 1-7 protein / TMEM85/ER membrane protein complex subunit 4 / Protein of unknown function (DUF1077) / ER membrane protein complex subunit 6 / ER membrane protein complex subunit 3 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 1 / ER membrane protein complex subunit 6-like / EMC6 / ER membrane protein complex subunit 1, C-terminal / Membrane magnesium transporter / ER membrane protein complex subunit 10 / ER membrane protein complex subunit 2-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily Similarity search - Domain/homology
ER membrane protein complex subunit 1 / ER membrane protein complex subunit 3 / Protein SOP4 / ER membrane protein complex subunit 5 / ER membrane protein complex subunit 2 / ER membrane protein complex subunit 4 / Endoplasmic reticulum membrane protein complex subunit 10 / ER membrane protein complex subunit 6 Similarity search - Component
National Institutes of Health/Office of the Director
1DP2OD017690-01
United States
Citation
Journal: Elife / Year: 2020 Title: Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J ...Authors: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J Shurtleff / Robert M Stroud / Charles S Craik / Brenda A Schulman / Adam Frost / Jonathan S Weissman / 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 ...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.
History
Deposition
Nov 24, 2020
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Header (metadata) release
Dec 2, 2020
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Map release
Dec 2, 2020
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Update
Dec 9, 2020
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Current status
Dec 9, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF Details: These two datasets were processed independently initially. Upon selecting the best subset of data and then re-extracted and scaled to the same pixel size and combined to get to the final 4.3 ...Details: These two datasets were processed independently initially. Upon selecting the best subset of data and then re-extracted and scaled to the same pixel size and combined to get to the final 4.3 A resolution maps and model. Number images used: 83599
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignment
Type: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)
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Image processing #2
Image processing ID
2
Image recording ID
2
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170186
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignment
Type: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Protocol: AB INITIO MODEL
Output model
PDB-7ktx: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent
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