+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vk0 | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of Hrd1-Usa1/Der1/Hrd3 of the flipped topology | ||||||
![]() |
| ||||||
![]() | PROTEIN TRANSPORT / retro-translocation / ERAD / protein degradation / ubiquitination | ||||||
Function / homology | ![]() Hrd1p ubiquitin ligase ERAD-M complex / ubiquitin-dependent glycoprotein ERAD pathway / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / misfolded protein transport / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / signal recognition particle binding / negative regulation of protein autoubiquitination ...Hrd1p ubiquitin ligase ERAD-M complex / ubiquitin-dependent glycoprotein ERAD pathway / detection of unfolded protein / luminal surveillance complex / Hrd1p ubiquitin ligase complex / misfolded protein transport / Hrd1p ubiquitin ligase ERAD-L complex / fungal-type cell wall organization / signal recognition particle binding / 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 K48-linked ubiquitination / protein autoubiquitination / 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Wu, X. / Rapoport, T.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 232.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 177 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 21222MC ![]() 6vjyC ![]() 6vjzC ![]() 6vk1C ![]() 6vk3C C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 39944.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: USA1 / Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 24411.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DER1 / Production host: ![]() ![]() |
#3: Protein | Mass: 88239.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HRD3 / Production host: ![]() ![]() |
#4: Protein | Mass: 55638.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: HRD1, DER3 / Production host: ![]() ![]() References: UniProt: Q08109, RING-type E3 ubiquitin transferase |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: complex of Hrd1-Usa1/Der1/Hrd3 of the flipped topology Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
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 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252744 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|