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Yorodumi- PDB-6vjz: CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vjz | ||||||
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Title | CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / retro-translocation / ERAD / protein degradation / ubiquitination | ||||||
Function / homology | Function and homology information Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / misfolded protein transport / Hrd1p ubiquitin ligase ERAD-L complex / signal recognition particle binding / fungal-type cell wall organization / negative regulation of protein autoubiquitination / misfolded protein binding ...Hrd1p ubiquitin ligase ERAD-M complex / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / misfolded protein transport / Hrd1p ubiquitin ligase ERAD-L complex / signal recognition particle binding / fungal-type cell wall organization / negative regulation of protein autoubiquitination / misfolded protein binding / positive regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / protein quality control for misfolded or incompletely synthesized proteins / protein autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / endoplasmic reticulum unfolded protein response / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / molecular adaptor activity / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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 | 6vjz.cif.gz | 221.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vjz.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vjz_validation.pdf.gz | 896.9 KB | Display | wwPDB validaton report |
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Full document | 6vjz_full_validation.pdf.gz | 928 KB | Display | |
Data in XML | 6vjz_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 6vjz_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/6vjz ftp://data.pdbj.org/pub/pdb/validation_reports/vj/6vjz | HTTPS FTP |
-Related structure data
Related structure data | 21221MC 6vjyC 6vk0C 6vk1C 6vk3C 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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-Components
#1: Protein | Mass: 24411.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DER1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38307 |
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#2: Protein | Mass: 55638.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HRD1, DER3 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q08109, RING-type E3 ubiquitin transferase |
#3: Protein | Mass: 88239.102 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 |
#4: Protein | Mass: 39944.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: USA1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03714 |
-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: complex of Hrd1-Usa1/Der1/Hrd3 in the expected topology 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.: 5 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: 54.8 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: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172291 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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