9Z0E | pdb_00009z0e

Structure of disulfide-crosslinked S. cerevisiae Hrd1 dimer bound to one copy of Hrd3 in MSP1D1 nanodisc

• PDB DOI: https://doi.org/10.2210/pdb9Z0E/pdb
• EM Map EMD-73699: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2025-10-31 Released: 2026-01-14 
• Deposition Author(s): Pisa, R., Rapoport, T.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI), American Heart Association

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Lipid bilayer thinning near a ubiquitin ligase selects ER membrane proteins for degradation

Pisa, R., Rapoport, T.A.

(2025) Bioarchive 

• DOI: https://doi.org/10.1101/2025.10.31.685944

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 174.05 kDa 
• Atom Count: 9,605 
• Modeled Residue Count: 1,163 
• Deposited Residue Count: 1,506 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERAD-associated E3 ubiquitin-protein ligase HRD1	A [auth B], B [auth C]	344	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: HRD1, DER3, YOL013C EC: 2.3.2.27
UniProt
Find proteins for Q08109 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08109  Go to UniProtKB:  Q08109

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ERAD-associated E3 ubiquitin-protein ligase component HRD3	C [auth A]	818	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HRD3, YLR207W
UniProt
Find proteins for Q05787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05787  Go to UniProtKB:  Q05787

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.7

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-01-14 
Deposition Author(s): Pisa, R., Rapoport, T.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GMO52586
Howard Hughes Medical Institute (HHMI)	United States	--
American Heart Association	United States	833683/2021
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1K99GM154114

Revision History  

• Version 1.0: 2026-01-14
  Type: Initial release