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Yorodumi- PDB-5v7v: Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5v7v | |||||||||
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Title | Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3 | |||||||||
Components | ERAD-associated E3 ubiquitin-protein ligase component HRD3 | |||||||||
Keywords | PROTEIN TRANSPORT / Hrd3 ERAD | |||||||||
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 / negative regulation of protein autoubiquitination / retrograde protein transport, ER to cytosol / : / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Mi, W. / Schoebel, S. / 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 |
-Downloads & links
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PDBx/mmCIF format | 5v7v.cif.gz | 222.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v7v.ent.gz | 180.7 KB | Display | PDB format |
PDBx/mmJSON format | 5v7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/5v7v ftp://data.pdbj.org/pub/pdb/validation_reports/v7/5v7v | HTTPS FTP |
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-Related structure data
Related structure data | 8642MC 8637C 8638C 8639C 5v6pC 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: 93759.156 Da / Num. of mol.: 1 / Fragment: UNP residues 1-767 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HRD3, YLR207W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05787 | ||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
-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/Hrd3 complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
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
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 1.4 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204578 / Symmetry type: POINT | ||||||||||||||||||||||||
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