2XK5

Crystal structure of K6-linked diubiquitin


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 par ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN
A
76Homo sapiensGene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN
B
76Homo sapiensGene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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 = 104.840α = 90.00
b = 104.840β = 90.00
c = 104.840γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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