Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.54 kDa 
• Atom Count: 1096 
• Residue Count: 148 
• Unique protein chains: 2

5KHY

Crystal structure of oxime-linked K6 diubiquitin

• DOI: 10.2210/pdb5KHY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Bacteria
• Mutation(s): No 


• Deposited: 2016-06-16 Released: 2016-09-14 
• Deposition Author(s): Stanley, M., Virdee, S.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.331 
• R-Value Work: 0.282 
• R-Value Observed: 0.295 

Literature

Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates.

Stanley, M., Virdee, S.

(2016) Chembiochem 17: 1472-1480

• PubMed: 27197715 
• DOI: 10.1002/cbic.201600138
• Primary Citation of Related Structures:  
  5KHY


• PubMed Abstract: 
  

We describe the genetically directed incorporation of aminooxy functionality into recombinant proteins by using a mutant Methanosarcina barkeri pyrrolysyl-tRNA synthetase/tRNACUA pair. This allows the general production of nonhydrolysable ubiquitin conjugates of recombinant origin by bioorthogonal oxime ligation. This was exemplified by the preparation of nonhydrolysable versions of diubiquitin, polymeric ubiquitin chains and ubiquitylated SUMO. The conjugates exhibited unrivalled isostery with the native isopeptide bond, as inferred from structural and biophysical characterisation. Furthermore, the conjugates functioned as nanomolar inhibitors of deubiquitylating enzymes and were recognised by linkage-specific antibodies. This technology should provide a versatile platform for the development of powerful tools for studying deubiquitylating enzymes and for elucidating the cellular roles of diverse polyubiquitin linkages.

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Organizational Affiliation: 

MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	73	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	75	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ETA	B	ETHANOLAMINE C2 H7 N O HZAXFHJVJLSVMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.331 
• R-Value Work: 0.282 
• R-Value Observed: 0.295 
• Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.975	α = 90
b = 103.975	β = 90
c = 103.975	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-16 
• Released Date: 2016-09-14 
Deposition Author(s): Stanley, M., Virdee, S.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_UU_12016/8

Revision History 

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Advisory, Author supporting evidence
• Version 1.2: 2018-11-21
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-10-16
  Changes: Data collection