+Open data
-Basic information
Entry | Database: PDB / ID: 6vk3 | ||||||
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Title | CryoEM structure of Hrd3/Yos9 complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / retro-translocation / ERAD / protein degradation / ubiquitination / glycan recognition | ||||||
Function / homology | Function and homology information Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / ubiquitin-dependent glycoprotein ERAD pathway / Hrd1p ubiquitin ligase ERAD-L complex / oligosaccharide binding / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / ERAD pathway ...Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / ubiquitin-dependent glycoprotein ERAD pathway / Hrd1p ubiquitin ligase ERAD-L complex / oligosaccharide binding / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / ERAD pathway / endoplasmic reticulum unfolded protein response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wu, X. / Rapoport, T.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2020 Title: Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Authors: Xudong Wu / Marc Siggel / Sergey Ovchinnikov / Wei Mi / Vladimir Svetlov / Evgeny Nudler / Maofu Liao / Gerhard Hummer / Tom A Rapoport / Abstract: Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD- ...Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo-electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two "half-channels" with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane. | ||||||
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 | 6vk3.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vk3.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vk3_validation.pdf.gz | 688.2 KB | Display | wwPDB validaton report |
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Full document | 6vk3_full_validation.pdf.gz | 702.5 KB | Display | |
Data in XML | 6vk3_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 6vk3_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/6vk3 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/6vk3 | HTTPS FTP |
-Related structure data
Related structure data | 21224MC 6vjyC 6vjzC 6vk0C 6vk1C 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
#1: Protein | Mass: 84328.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Hrd3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05787*PLUS |
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#2: Protein | Mass: 61311.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YOS9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q99220 |
Sequence details | The full sequence of poly-UNK region in HRD3 is PDIGSPFIAQVNGVQMTLQIEPMGRFAFNGNDGNINGDEDDE, UniProt ...The full sequence of poly-UNK region in HRD3 is PDIGSPFIAQ |
-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: a complex of Hrd1/Hrd3/Yos9 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
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: OTHER |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 44.9 e/Å2 / Film or detector model: GATAN K3 (6k 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: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99298 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.7 Å | ||||||||||||||||||||||||
Refine LS restraints |
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