› 6vk0

Electron Microscopy
4.1Å resolution

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

Released:
DOI: 10.2210/pdb6vk0/pdb
PDB entry 6vk0 coloured by chain, front view.
PDB entry 6vk0 coloured by chain, side view.
PDB entry 6vk0 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
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 TA
Science 368 (2020)
PMID: 32327568
Related structures: EMD-21222

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-153606 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
U1 SNP1-associating protein 1 Chain: D
Molecule details ›
Chain: D
Length: 339 amino acids
Theoretical weight: 39.94 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03714 (Residues: 500-838; Coverage: 41%)
Gene names: USA1, YML029W
Degradation in the endoplasmic reticulum protein 1 Chain: C
Molecule details ›
Chain: C
Length: 211 amino acids
Theoretical weight: 24.41 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38307 (Residues: 1-211; Coverage: 100%)
Gene names: DER1, YBR1413, YBR201W
Sequence domains: Der1-like family
ERAD-associated E3 ubiquitin-protein ligase component HRD3 Chain: A
Molecule details ›
Chain: A
Length: 767 amino acids
Theoretical weight: 88.24 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q05787 (Residues: 1-767; Coverage: 92%)
Gene names: HRD3, YLR207W
Sequence domains: Sel1 repeat
ERAD-associated E3 ubiquitin-protein ligase HRD1 Chain: B
Molecule details ›
Chain: B
Length: 480 amino acids
Theoretical weight: 55.64 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08109 (Residues: 1-480; Coverage: 87%)
Gene names: DER3, HRD1, YOL013C
Sequence domains: Ring finger domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-21222
Expression system: Saccharomyces cerevisiae

Quick links

Citations

32 review citations

A guide to understanding endoplasmic reticulum stress in metabolic disorders.
Lemmer et al. (2021)
31 more

2 mentions without citation

Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.
Wu et al. (2020)
1 more