Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 23.01 kDa 
• Atom Count: 1527 
• Residue Count: 178 
• Unique protein chains: 1

2Y43

Rad18 ubiquitin ligase RING domain structure

• DOI: 10.2210/pdb2Y43/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-05-11 
• Deposition Author(s): Hibbert, R.G., Sixma, T.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Symmetry and Asymmetry of the Ring-Ring Dimer of Rad18.

Huang, A., Hibbert, R.G., De Jong, R.N., Das, D., Sixma, T.K., Boelens, R.

(2011) J Mol Biol 410: 424

• PubMed: 21549715 
• DOI: 10.1016/j.jmb.2011.04.051
• Primary Citation of Related Structures:  
  2Y43, 2Y4W


• PubMed Abstract: 
  

The human ubiquitin-conjugating enzyme Rad6 (E2), with ubiquitin ligase enzyme Rad18 (RING E3), monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Here, we determine the structure of the homodimeric Rad18 RING domains by X-ray crystallography and classify it to RING-RING dimers that dimerize through helices adjacent to the RING domains and through the canonical RING domains. Using NMR spectroscopy and site-directed mutagenesis, we demonstrate that the Rad6b binding site, for the Rad18 RING domain, strongly resembles that of other E2/E3 RING/U-box complexes. We show that the homodimeric Rad18 RING domain can recruit two Rad6b E2 enzymes, whereas the full-length Rad18 homodimer binds only to a single Rad6b molecule. Such asymmetry is a common feature of RING-RING heterodimers and has been observed for the CHIP U-box homodimer. We propose that asymmetry may be a common feature of dimeric RING E3 ligases.

---

Organizational Affiliation: 

Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE RAD18	A, B	99	Homo sapiens	Mutation(s): 0  Gene Names: RAD18, RNF73 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q9NS91 (Homo sapiens) Explore Q9NS91  Go to UniProtKB:  Q9NS91
NIH Common Fund Data Resources
PHAROS:  Q9NS91 GTEx:  ENSG00000070950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.646	α = 90
b = 29.357	β = 125.05
c = 69.736	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
SHELX	phasing
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-04 
• Released Date: 2011-05-11 
Deposition Author(s): Hibbert, R.G., Sixma, T.K.

Revision History 

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-06-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance