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Yorodumi- PDB-7adp: Cryo-EM structure of human ER membrane protein complex in GDN det... -
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-Basic information
Entry | Database: PDB / ID: 7adp | |||||||||
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Title | Cryo-EM structure of human ER membrane protein complex in GDN detergent | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ER membrane protein / EMC / Membrane protein biogenesis | |||||||||
Function / homology | Function and homology information extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / protein folding in endoplasmic reticulum / copper ion transport / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / angiogenesis / early endosome / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Braeuning, B. / Prabu, J.R. / Miller-Vedam, L.E. / Weissman, J.S. / Frost, A. / Schulman, B.A. | |||||||||
Funding support | Germany, 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 | 7adp.cif.gz | 349 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7adp.ent.gz | 282.7 KB | Display | PDB format |
PDBx/mmJSON format | 7adp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7adp_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7adp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7adp_validation.xml.gz | 64.5 KB | Display | |
Data in CIF | 7adp_validation.cif.gz | 95.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7adp ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7adp | HTTPS FTP |
-Related structure data
Related structure data | 11733MC 7adoC 7kraC 7ktxC 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 ... , 7 types, 7 molecules ABCDFHI
#1: Protein | Mass: 111886.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC1, KIAA0090, PSEC0263 / Plasmid: pEG / Cell line (production host): HEK 293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8N766 |
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#2: Protein | Mass: 34882.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC2, KIAA0103, TTC35 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q15006 |
#3: Protein | Mass: 29981.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC3, TMEM111 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9P0I2 |
#4: Protein | Mass: 20104.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: No mutation; again, as for D_1292111207 there is failed alignment between structure and sequence. Please see communication, thanks! Source: (gene. exp.) Homo sapiens (human) / Gene: EMC4, TMEM85, HSPC184, PIG17 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q5J8M3 |
#6: Protein | Mass: 12029.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC6, TMEM93 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9BV81 |
#7: Protein | Mass: 23807.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC8, C16orf2, C16orf4, COX4AL, COX4NB, FAM158B, NOC4 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: O43402 |
#8: Protein | Mass: 27446.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMC10, C19orf63, HSM1, INM02, UNQ764/PRO1556 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q5UCC4 |
-Protein / Sugars , 2 types, 4 molecules E
#5: Protein | Mass: 15703.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMGT1, EMC5, TMEM32 / Plasmid: pEG / Cell line (production host): HEK 293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8N4V1 |
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#9: Sugar |
-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
Component | Name: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Molecular weight | Value: 0.3 MDa |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK293 GnTI- / Plasmid: pEG |
Buffer solution | pH: 6 Details: 10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 16, 2019 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 5 sec. / Electron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144222 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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