9DNP | pdb_00009dnp

Structure of UBR2-RFF complex

• PDB DOI: https://doi.org/10.2210/pdb9DNP/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: 1.22 Å
• R-Value Free: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structural Flexibility and Selectivity of N-End Rule Ligases

Huang, S., 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: 17.49 kDa 
• Atom Count: 1,407 
• Modeled Residue Count: 153 
• Deposited Residue Count: 154 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UBR2	A, C [auth B]	73	Homo sapiens	Mutation(s): 0  Gene Names: UBR2, C6orf133, KIAA0349 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWV8 (Homo sapiens) Explore Q8IWV8  Go to UniProtKB:  Q8IWV8
PHAROS:  Q8IWV8 GTEx:  ENSG00000024048

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-PHE-PHE-NH2	B [auth C], D	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: 1.22 Å
• R-Value Free:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.538	α = 90
b = 56.987	β = 90
c = 115.606	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
DIALS	data reduction
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 CA212119
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA265410

Revision History  

• Version 1.0: 2025-08-13
  Type: Initial release