Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17377.75 
• Atom Count: 1199 
• Residue Count: 152 
• Unique protein chains: 1

4ZPZ

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

• DOI: 10.2210/pdb4ZPZ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


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

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Experimental Data Snapshot

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

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

• PubMed: 26010437 
• 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 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.

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Organizational Affiliation: 

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
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	A, B	76	Homo sapiens	Mutation(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
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

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 = 41.699	α = 90.00
b = 41.699	β = 90.00
c = 69.831	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-08 
• Released Date: 2015-06-10 
• Deposition Author(s): Han, C., Virdee, S.

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Funding Organization	Location	Grant 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