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

Structural Flexibility and Selectivity of N-End Rule Ligases

Huang, S.T., Wu, J., Taylor, S., Chen, Y.

To be published.

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