8P82

Cryo-EM structure of dimeric UBR5


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Tsai, J.M.Aguirre, J.D.Li, Y.D.Brown, J.Focht, V.Kater, L.Kempf, G.Sandoval, B.Schmitt, S.Rutter, J.C.Galli, P.Sandate, C.R.Cutler, J.A.Zou, C.Donovan, K.A.Lumpkin, R.J.Cavadini, S.Park, P.M.C.Sievers, Q.Hatton, C.Ener, E.Regalado, B.D.Sperling, M.T.Slabicki, M.Kim, J.Zon, R.Zhang, Z.Miller, P.G.Belizaire, R.Sperling, A.S.Fischer, E.S.Irizarry, R.Armstrong, S.A.Thoma, N.H.Ebert, B.L.

(2023) Mol Cell 83: 2753-2767.e10

  • DOI: https://doi.org/10.1016/j.molcel.2023.06.028
  • Primary Citation of Related Structures:  
    8P82, 8P83

  • PubMed Abstract: 

    Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.


  • Organizational Affiliation

    Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UBR5
A, B
2,831Homo 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
GTEx:  ENSG00000104517 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95071
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland179541
Swiss National Science FoundationSwitzerland201206
European Research Council (ERC)European Union884331

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Data collection, Database references