5V7V

Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3

• PDB DOI: https://doi.org/10.2210/pdb5V7V/pdb
• EM Map EMD-8642: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2017-03-20 Released: 2017-08-16 
• Deposition Author(s): Mi, W., Schoebel, S., Stein, A., Rapoport, T.A., Liao, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 95.6 kDa 
• Atom Count: 5,108 
• Modelled Residue Count: 613 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERAD-associated E3 ubiquitin-protein ligase component HRD3	A	818	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HRD3, YLR207W Membrane Entity: Yes
UniProt
Find proteins for Q05787 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05787  Go to UniProtKB:  Q05787

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Mi, W., Schoebel, S., Stein, A., Rapoport, T.A., Liao, M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM052586

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Author supporting evidence, Database references
• Version 1.2: 2017-08-30
  Changes: Database references
• Version 1.3: 2018-07-18
  Changes: Data collection, Experimental preparation
• Version 1.4: 2020-01-01
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary