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Yorodumi- PDB-5v6p: CryoEM structure of the ERAD-associated E3 ubiquitin-protein liga... -
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-Basic information
Entry | Database: PDB / ID: 5v6p | ||||||
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Title | CryoEM structure of the ERAD-associated E3 ubiquitin-protein ligase HRD1 | ||||||
Components | ERAD-associated E3 ubiquitin-protein ligase HRD1 | ||||||
Keywords | TRANSFERASE / Retrotranslocon / E3 ligase / ERAD | ||||||
Function / homology | Function and homology information Hrd1p ubiquitin ligase ERAD-M complex / Hrd1p ubiquitin ligase complex / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / retrograde protein transport, ER to cytosol / protein K48-linked ubiquitination / protein autoubiquitination / endoplasmic reticulum unfolded protein response / : / RING-type E3 ubiquitin transferase ...Hrd1p ubiquitin ligase ERAD-M complex / Hrd1p ubiquitin ligase complex / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / retrograde protein transport, ER to cytosol / protein K48-linked ubiquitination / protein autoubiquitination / endoplasmic reticulum unfolded protein response / : / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Schoebel, S. / Mi, W. / Stein, A. / Rapoport, T.A. / Liao, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2017 Title: Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Authors: Stefan Schoebel / Wei Mi / Alexander Stein / Sergey Ovchinnikov / Ryan Pavlovicz / Frank DiMaio / David Baker / Melissa G Chambers / Huayou Su / Dongsheng Li / Tom A Rapoport / Maofu Liao / Abstract: Misfolded endoplasmic reticulum proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the membrane, and degraded by the proteasome-a ...Misfolded endoplasmic reticulum proteins are retro-translocated through the membrane into the cytosol, where they are poly-ubiquitinated, extracted from the membrane, and degraded by the proteasome-a pathway termed endoplasmic reticulum-associated protein degradation (ERAD). Proteins with misfolded domains in the endoplasmic reticulum lumen or membrane are discarded through the ERAD-L and ERAD-M pathways, respectively. In Saccharomyces cerevisiae, both pathways require the ubiquitin ligase Hrd1, a multi-spanning membrane protein with a cytosolic RING finger domain. Hrd1 is the crucial membrane component for retro-translocation, but it is unclear whether it forms a protein-conducting channel. Here we present a cryo-electron microscopy structure of S. cerevisiae Hrd1 in complex with its endoplasmic reticulum luminal binding partner, Hrd3. Hrd1 forms a dimer within the membrane with one or two Hrd3 molecules associated at its luminal side. Each Hrd1 molecule has eight transmembrane segments, five of which form an aqueous cavity extending from the cytosol almost to the endoplasmic reticulum lumen, while a segment of the neighbouring Hrd1 molecule forms a lateral seal. The aqueous cavity and lateral gate are reminiscent of features of protein-conducting conduits that facilitate polypeptide movement in the opposite direction-from the cytosol into or across membranes. Our results suggest that Hrd1 forms a retro-translocation channel for the movement of misfolded polypeptides through the endoplasmic reticulum membrane. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5v6p.cif.gz | 197.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v6p.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 5v6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/5v6p ftp://data.pdbj.org/pub/pdb/validation_reports/v6/5v6p | HTTPS FTP |
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-Related structure data
Related structure data | 8637MC 8638C 8639C 8642C 5v7vC 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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-Components
#1: Protein | Mass: 47866.418 Da / Num. of mol.: 2 / Fragment: UNP residues 1-407 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HRD1, DER3, YOL013C / Plasmid: pRS426 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: Q08109, RING-type E3 ubiquitin transferase |
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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: Hrd1 dimer in Hrd1/Hrd3 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Source (recombinant) | Organism: Saccharomyces (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.8 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 82 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: GeRelion / Version: 1 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93609 / Symmetry type: POINT |