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Yorodumi- PDB-7ktx: Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein... -
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-Basic information
Entry | Database: PDB / ID: 7ktx | |||||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae ER membrane protein complex bound to a Fab in DDM detergent | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN/IMMUNE SYSTEM / ER membrane protein complex / EMC / membrane protein biogenesis / insertase / chaperone / endoplasmic / reticulum / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) Saccharomyces cerevisiae BY4743 (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Miller-Vedam, L.E. / Schirle Oakdale, N.S. / Braeuning, B. / Boydston, E.A. / Sevillano, N. / Popova, K.D. / Bonnar, J.L. / Shurtleff, M.J. / Prabu, J.R. / Stroud, R.M. ...Miller-Vedam, L.E. / Schirle Oakdale, N.S. / Braeuning, B. / Boydston, E.A. / Sevillano, N. / Popova, K.D. / Bonnar, J.L. / Shurtleff, M.J. / Prabu, J.R. / Stroud, R.M. / Craik, C.S. / Schulman, B.A. / Weissman, J.S. / Frost, A. | |||||||||
Funding support | United States, 2items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ktx.cif.gz | 401.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ktx.ent.gz | 323 KB | Display | PDB format |
PDBx/mmJSON format | 7ktx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/7ktx ftp://data.pdbj.org/pub/pdb/validation_reports/kt/7ktx | HTTPS FTP |
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-Related structure data
Related structure data | 23033MC 7adoC 7adpC 7kraC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ER membrane protein complex subunit ... , 6 types, 6 molecules ABCDEF
#1: Protein | Mass: 87272.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P25574 |
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#2: Protein | Mass: 33893.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P47133 |
#3: Protein | Mass: 28372.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P36039 |
#4: Protein | Mass: 21478.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P53073 |
#5: Protein | Mass: 20489.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P40540 |
#6: Protein | Mass: 12411.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: Q12431 |
-Protein , 2 types, 2 molecules GH
#7: Protein | Mass: 26627.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: P39543 |
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#8: Protein | Mass: 22792.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 / References: UniProt: Q12025 |
-Antibody , 2 types, 2 molecules IJ
#9: Antibody | Mass: 26849.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG |
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#10: Antibody | Mass: 25566.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG |
-Protein/peptide / Sugars , 2 types, 8 molecules MN
#11: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae BY4743 (yeast) / Strain: BY4743 #12: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain: BL21-Gold(DE3)pLysS AG | ||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company / Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELDBright-field microscopy / Specimen-ID: 1
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Image recording |
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-Processing
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EM software |
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Image processing |
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CTF correction |
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3D reconstruction | Entry-ID: 7KTX / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 167.41 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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