Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.84 kDa 
• Atom Count: 1532 
• Residue Count: 171 
• Unique protein chains: 2

2YBF

Complex of Rad18 (Rad6 binding domain) with Rad6b

• DOI: 10.2210/pdb2YBF/pdb

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


• Deposited: 2011-03-08 Released: 2011-04-20 
• Deposition Author(s): Hibbert, R.G., Sixma, T.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.

Hibbert, R.G., Huang, A., Boelens, R., Sixma, T.K.

(2011) Proc Natl Acad Sci U S A 108: 5590

• PubMed: 21422291 
• DOI: 10.1073/pnas.1017516108
• Primary Citation of Related Structures:  
  2YB6, 2YBF


• PubMed Abstract: 
  

In ubiquitin conjugation, different combinations of E2 and E3 enzymes catalyse either monoubiquitination or ubiquitin chain formation. The E2/E3 complex Rad6/Rad18 exclusively monoubiquitinates the proliferating cell nuclear antigen (PCNA) to signal for "error prone" DNA damage tolerance, whereas a different set of conjugation enzymes is required for ubiquitin chain formation on PCNA. Here we show that human E2 enzyme Rad6b is intrinsically capable of catalyzing ubiquitin chain formation. This activity is prevented during PCNA ubiquitination by the interaction of Rad6 with E3 enzyme Rad18. Using NMR and X-ray crystallography we show that the R6BD of Rad18 inhibits this activity by competing with ubiquitin for a noncovalent "backside" binding site on Rad6. Our findings provide mechanistic insights into how E3 enzymes can regulate the ubiquitin conjugation process.

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Organizational Affiliation: 

Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 B	A	152	Homo sapiens	Mutation(s): 0  Gene Names: UBE2B, RAD6B EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P63146 (Homo sapiens) Explore P63146  Go to UniProtKB:  P63146
NIH Common Fund Data Resources
PHAROS:  P63146 GTEx:  ENSG00000119048

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE RAD18	B	27	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.21	α = 90
b = 58.21	β = 90
c = 167.07	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-08 
• Released Date: 2011-04-20 
Deposition Author(s): Hibbert, R.G., Sixma, T.K.

Revision History 

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance