8EWI

Structure of the human UBR5 HECT-type E3 ubiquitin ligase in a tetrameric form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the human UBR5 E3 ubiquitin ligase.

Wang, F.He, Q.Zhan, W.Yu, Z.Finkin-Groner, E.Ma, X.Lin, G.Li, H.

(2023) Structure 31: 541-552.e4

  • DOI: https://doi.org/10.1016/j.str.2023.03.010
  • Primary Citation of Related Structures:  
    8D4X, 8E0Q, 8EWI

  • PubMed Abstract: 

    The human UBR5 is a single polypeptide chain homology to E6AP C terminus (HECT)-type E3 ubiquitin ligase essential for embryonic development in mammals. Dysregulated UBR5 functions like an oncoprotein to promote cancer growth and metastasis. Here, we report that UBR5 assembles into a dimer and a tetramer. Our cryoelectron microscopy (cryo-EM) structures reveal that two crescent-shaped UBR5 monomers assemble head to tail to form the dimer, and two dimers bind face to face to form the cage-like tetramer with all four catalytic HECT domains facing the central cavity. Importantly, the N-terminal region of one subunit and the HECT of the other form an "intermolecular jaw" in the dimer. We show the jaw-lining residues are important for function, suggesting that the intermolecular jaw functions to recruit ubiquitin-loaded E2 to UBR5. Further work is needed to understand how oligomerization regulates UBR5 ligase activity. This work provides a framework for structure-based anticancer drug development and contributes to a growing appreciation of E3 ligase diversity.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UBR5
A, B, C, D
2,799Homo sapiensMutation(s): 0 
Gene Names: UBR5EDDEDD1HYDKIAA0896
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95071
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth B]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2023-05-17
    Changes: Database references
  • Version 1.3: 2024-06-19
    Changes: Data collection