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 6VK0 | pdb_00006vk0

CryoEM structure of Hrd1-Usa1/Der1/Hrd3 of the flipped topology


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6VK0

This is version 1.2 of the entry. See complete history. 

Literature

Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.

Wu, X., Siggel, M., Ovchinnikov, S., Mi, W., Svetlov, V., Nudler, E., Liao, M., Hummer, G., Rapoport, T.A.

(2020) Science 368

  • DOI: https://doi.org/10.1126/science.aaz2449
  • Primary Citation Related Structures: 
    6VJY, 6VJZ, 6VK0, 6VK1, 6VK3

  • PubMed 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-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.


  • Organizational Affiliation: 
    • Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 208.23 kDa 
  • Atom Count: 9,559 
  • Modeled Residue Count: 1,160 
  • Deposited Residue Count: 1,797 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
U1 SNP1-associating protein 1A [auth D]339Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: USA1
Membrane Entity: Yes 
UniProt
Find proteins for Q03714 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03714 
Go to UniProtKB:  Q03714
Entity Groups
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UniProt GroupQ03714
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Degradation in the endoplasmic reticulum protein 1B [auth C]211Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DER1
Membrane Entity: Yes 
UniProt
Find proteins for P38307 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38307 
Go to UniProtKB:  P38307
Entity Groups
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UniProt GroupP38307
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ERAD-associated E3 ubiquitin-protein ligase component HRD3C [auth A]767Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HRD3
Membrane Entity: Yes 
UniProt
Find proteins for Q05787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05787 
Go to UniProtKB:  Q05787
Entity Groups
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UniProt GroupQ05787
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ERAD-associated E3 ubiquitin-protein ligase HRD1D [auth B]480Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HRD1, DER3
EC: 2.3.2.27
Membrane Entity: Yes 
UniProt
Find proteins for Q08109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08109 
Go to UniProtKB:  Q08109
Entity Groups
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UniProt GroupQ08109
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM052586

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references