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 
  • R-Value Observed: 0.140 

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
  • Primary Citation of Related Structures:  
    4ZPZ

  • 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 E3 l ...

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B A, B76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		A,BL-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 
  • R-Value Observed: 0.140 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.699α = 90
b = 41.699β = 90
c = 69.831γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence