8P82

Cryo-EM structure of dimeric UBR5

• PDB DOI: https://doi.org/10.2210/pdb8P82/pdb
• EM Map EMD-17539: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-05-31 Released: 2023-06-14 
• Deposition Author(s): Aguirre, J.D., Kater, L., Kempf, G., Cavadini, S., Thoma, N.H.
• Funding Organization(s): Swiss National Science Foundation, European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability

Na, N.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 626.92 kDa 
• Atom Count: 25,156 
• Modelled Residue Count: 3,192 
• Deposited Residue Count: 5,662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UBR5	A, B	2,831	Homo sapiens	Mutation(s): 0  Gene Names: UBR5, EDD, EDD1, HYD, KIAA0896 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for O95071 (Homo sapiens) Explore O95071  Go to UniProtKB:  O95071
PHAROS:  O95071 GTEx:  ENSG00000104517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Aguirre, J.D., Kater, L., Kempf, G., Cavadini, S., Thoma, N.H.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	179541
Swiss National Science Foundation	Switzerland	201206
European Research Council (ERC)	European Union	884331

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release