Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 17624.57 
• Atom Count: 1121 
• Residue Count: 152 
• Unique protein chains: 2

2XK5

Crystal structure of K6-linked diubiquitin

• DOI: 10.2210/pdb2XK5/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-07-07 Released: 2010-08-25 
• Deposition Author(s): Virdee, S., Chin, J.W., Komander, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 

Literature

Engineered Diubiquitin Synthesis Reveals K29-Isopeptide Specificity of an Otu Deubiquitinase

Virdee, S., Ye, Y., Nguyen, D.P., Komander, D., Chin, J.W.

(2010) Nat.Chem.Biol. 6: 750

• PubMed: 20802491 
• DOI: 10.1038/nchembio.426


• PubMed Abstract: 
  

Ubiquitination is a reversible post-translational modification that regulates a myriad of eukaryotic functions. Our ability to study the effects of ubiquitination is often limited by the inaccessibility of homogeneously ubiquitinated proteins. In particular, elucidating the roles of the so-called 'atypical' ubiquitin chains (chains other than Lys48- or Lys63-linked ubiquitin), which account for a large fraction of ubiquitin polymers, is challenging because the enzymes for their biosynthesis are unknown. Here we combine genetic code expansion, intein chemistry and chemoselective ligations to synthesize 'atypical' ubiquitin chains. We solve the crystal structure of Lys6-linked diubiquitin, which is distinct from that of structurally characterized ubiquitin chains, providing a molecular basis for the different biological functions this linkage may regulate. Moreover, we profile a panel containing 10% of the known human deubiquitinases on Lys6- and Lys29-linked ubiquitin and discover that TRABID cleaves the Lys29 linkage 40-fold more efficiently than the Lys63 linkage.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, England, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN	A	76	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN	B	76	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
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• Space Group: P 4₃ 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 104.840	α = 90.00
b = 104.840	β = 90.00
c = 104.840	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-07 
• Released Date: 2010-08-25 
• Deposition Author(s): Virdee, S., Chin, J.W., Komander, D.

Revision History 

• Version 1.0: 2010-08-25
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance