+Open data
-Basic information
Entry | Database: PDB / ID: 6wb9 | ||||||
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Title | Structure of the S. cerevisiae ER membrane complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / insertase / complex / ER | ||||||
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 / phospholipid metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / 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 / phospholipid metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / protein-folding chaperone binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae W303 (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Bai, L. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2020 Title: Structure of the ER membrane complex, a transmembrane-domain insertase. Authors: Lin Bai / Qinglong You / Xiang Feng / Amanda Kovach / Huilin Li / 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 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. 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, 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wb9.cif.gz | 333 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wb9.ent.gz | 270.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wb9_validation.pdf.gz | 816.7 KB | Display | wwPDB validaton report |
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Full document | 6wb9_full_validation.pdf.gz | 845.7 KB | Display | |
Data in XML | 6wb9_validation.xml.gz | 53.9 KB | Display | |
Data in CIF | 6wb9_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/6wb9 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wb9 | HTTPS FTP |
-Related structure data
Related structure data | 21587MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules 07
#1: Protein | Mass: 22792.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12025 |
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#8: Protein | Mass: 26627.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P39543 |
-ER membrane protein complex subunit ... , 6 types, 6 molecules 123456
#2: Protein | Mass: 87272.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P25574 |
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#3: Protein | Mass: 33893.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P47133 |
#4: Protein | Mass: 28372.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P36039 |
#5: Protein | Mass: 21478.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P53073 |
#6: Protein | Mass: 15926.407 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P40540 |
#7: Protein | Mass: 12401.341 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast) / Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q12431 |
-Sugars / Non-polymers , 2 types, 8 molecules
#10: Chemical | #9: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ER Membrane Complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae W303 (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae W303 (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 590118 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355991 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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