Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28628.86 
• Atom Count: 1723 
• Residue Count: 250 
• Unique protein chains: 2

4R62

Structure of Rad6~Ub

• DOI: 10.2210/pdb4R62/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2014-08-22 Released: 2015-09-02 
• Deposition Author(s): Kumar, P., Wolberger, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 

Literature

Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity.

Kumar, P., Magala, P., Geiger-Schuller, K.R., Majumdar, A., Tolman, J.R., Wolberger, C.

(2015) Nucleic Acids Res. 43: 9039-9050

• PubMed: 26286193 
• DOI: 10.1093/nar/gkv845


• PubMed Abstract: 
  

Rad6 is a yeast E2 ubiquitin conjugating enzyme that monoubiquitinates histone H2B in conjunction with the E3, Bre1, but can non-specifically modify histones on its own. We determined the crystal structure of a Rad6∼Ub thioester mimic, which revealed a network of interactions in the crystal in which the ubiquitin in one conjugate contacts Rad6 in another. The region of Rad6 contacted is located on the distal face of Rad6 opposite the active site, but differs from the canonical E2 backside that mediates free ubiquitin binding and polyubiquitination activity in other E2 enzymes. We find that free ubiquitin interacts weakly with both non-canonical and canonical backside residues of Rad6 and that mutations of non-canonical residues have deleterious effects on Rad6 activity comparable to those observed to mutations in the canonical E2 backside. The effect of non-canonical backside mutations is similar in the presence and absence of Bre1, indicating that contacts with non-canonical backside residues govern the intrinsic activity of Rad6. Our findings shed light on the determinants of intrinsic Rad6 activity and reveal new ways in which contacts with an E2 backside can regulate ubiquitin conjugating activity.

---

Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 2	A	172	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 1  Gene Names: RAD6 (UBC2) EC: 2.3.2.23
Find proteins for P06104 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P06104

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-40S ribosomal protein S27a	B	78	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens) Go to Gene View: RPS27A Go to UniProtKB:  P62979

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.265 
• R-Value Work: 0.210 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 33.666	α = 90.00
b = 58.412	β = 90.00
c = 115.722	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
HKL-3000	data collection
PHENIX	phasing
HKL-3000	data scaling
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-22 
• Released Date: 2015-09-02 
• Deposition Author(s): Kumar, P., Wolberger, C.

Revision History 

• Version 1.0: 2015-09-02
  Type: Initial release
• Version 1.1: 2015-10-28
  Type: Database references