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- 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 | ||||||
![]() | ERAD-associated E3 ubiquitin-protein ligase HRD1 | ||||||
![]() | TRANSFERASE / Retrotranslocon / E3 ligase / ERAD | ||||||
Function / homology | ![]() 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 autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / 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 autoubiquitination / protein K48-linked ubiquitination / ERAD pathway / 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 / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Schoebel, S. / Mi, W. / Stein, A. / Rapoport, T.A. / Liao, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
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PDBx/mmCIF format | ![]() | 197.9 KB | Display | ![]() |
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PDB format | ![]() | 156.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 962.3 KB | Display | ![]() |
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Full document | ![]() | 962.4 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8637MC ![]() 8638C ![]() 8639C ![]() 8642C ![]() 5v7vC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HRD1, DER3, YOL013C / Plasmid: pRS426 / Production host: ![]() ![]() 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 |
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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: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 82 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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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 |