4ZPZ

Crystal Structure of Semi-synthetic Ubiquitin with Phospho-Ser65 and Ala46Cys

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

A Versatile Strategy for the Semisynthetic Production of Ser65 Phosphorylated Ubiquitin and Its Biochemical and Structural Characterisation.

Han, C., Pao, K.C., Kazlauskaite, A., Muqit, M.M., Virdee, S.

(2015) Chembiochem 16: 1574-1579

  • DOI: 10.1002/cbic.201500185

  • PubMed Abstract: 

    • Ubiquitin phosphorylation is emerging as an important regulatory layer in the ubiquitin system. This is exemplified by the phosphorylation of ubiquitin on Ser65 by the Parkinson's disease-associated kinase PINK1, which mediates the activation of the ...

    Ubiquitin phosphorylation is emerging as an important regulatory layer in the ubiquitin system. This is exemplified by the phosphorylation of ubiquitin on Ser65 by the Parkinson's disease-associated kinase PINK1, which mediates the activation of the E3 ligase Parkin. Additional phosphorylation sites on ubiquitin might also have important cellular roles. Here we report a versatile strategy for preparing phosphorylated ubiquitin. We biochemically and structurally characterise semisynthetic phospho-Ser65-ubiquitin. Unexpectedly, we observed disulfide bond formation between ubiquitin molecules, and hence a novel crystal form. The method outlined provides a direct approach to study the combinatorial effects of phosphorylation on ubiquitin function. Our analysis also suggests that disulfide engineering of ubiquitin could be a useful strategy for obtaining alternative crystal forms of ubiquitin species thereby facilitating structural validation.

    Organizational Affiliation: 

    MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK). s.s.virdee@dundee.ac.uk.,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
A, B
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.139 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 41.699α = 90.00
b = 41.699β = 90.00
c = 69.831γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-05-08 
  • Released Date: 2015-06-10 
  • Deposition Author(s): Han, C., Virdee, S.
Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence