9DNO | pdb_00009dno

Structure of UBR1-RFF complex

• PDB DOI: https://doi.org/10.2210/pdb9DNO/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-17 Released: 2025-08-13 
• Deposition Author(s): Huang, S., Wu, J., Taylor, S., Chen, Y.
• Funding Organization(s): Department of Defense (DOD, United States), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

An alternative pocket for binding the N-degrons by the UBR1 and UBR2 ubiquitin E3 ligases.

Huang, S.T., Chen, D.H., Ren, T., Thomas, N., Wu, J., Sankaran, B., Jones, R., Taylor, S., Chen, Y.

(2025) Protein Sci 34: e70248-e70248

• PubMed: 40880185 
• DOI: https://doi.org/10.1002/pro.70248
• Primary Citation Related Structures: 
  9DNO, 9DNP, 9DNQ, 9DNR, 9MUX


• PubMed Abstract: 
  

  The UBR family of ubiquitin ligases binds to N-termini of their targets (known as N-degron) to induce their ubiquitination and degradation via a conserved domain known as UBR-box. UBR1 and UBR2 share the highest sequence homology among the family, and substantial structural studies were previously performed for substrate binding by the UBR-boxes of UBR1 and UBR2. Here, we describe a new pocket in the UBR-boxes of UBR1 and UBR2 for binding the second residues of N-degrons through determining five co-crystal structures of the UBR-boxes with various N-degron peptides. Together with binding affinities measured by fluorescence polarization, we show that the two highly homologous UBR-boxes can interact with the second residue of an N-degron differently. In addition, the UBR-boxes undergo different conformational changes when binding N-degrons. Furthermore, we demonstrate that the sidechain of the third amino acid of an N-degron has no contribution to binding the UBR-boxes. These findings represent a new conceptual advancement for the UBR E3 ligases and the new insights described here can be leveraged for developing their selective ligands for research and potential therapies.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
Division of Surgical Sciences, Moores Cancer Center, University of California, San Diego, La Jolla, California, USA.
Department of Pharmacology, University of California, San Diego, La Jolla, California, USA.
Molecular Biophysics and Integrated Bioimaging Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Department of Surgery, University of California, San Diego, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.23 kDa 
• Atom Count: 1,380 
• Modeled Residue Count: 156 
• Deposited Residue Count: 162 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UBR1	A, B	77	Homo sapiens	Mutation(s): 0  Gene Names: UBR1 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWV7 (Homo sapiens) Explore Q8IWV7  Go to UniProtKB:  Q8IWV7
PHAROS:  Q8IWV7 GTEx:  ENSG00000159459

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-PHE-PHE-NH2	C [auth D], D [auth E]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.507	α = 90
b = 48.952	β = 106.85
c = 49.946	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-13 
Deposition Author(s): Huang, S., Wu, J., Taylor, S., Chen, Y.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	HT9425-23-1-0560
Department of Defense (DOD, United States)	United States	PA220024P1
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA265410
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA212119

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release
  
• Version 1.1: 2026-02-25
  Changes: Database references