Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 8.66 kDa 
• Atom Count: 691 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

5K9P

Ser20 phosphorylated ubiquitin

• PDB DOI: 10.2210/pdb5K9P/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-07-20 
• Deposition Author(s): Huguenin-Dezot, N., Chin, J.W.
• Funding Organization(s): Medical Research Council (United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.219 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity.

Huguenin-Dezot, N., De Cesare, V., Peltier, J., Knebel, A., Kristaryianto, Y.A., Rogerson, D.T., Kulathu, Y., Trost, M., Chin, J.W.

(2016) Cell Rep 16: 1180-1193

• PubMed: 27425610 
• DOI: 10.1016/j.celrep.2016.06.064
• Primary Citation of Related Structures:  
  5K9P


• PubMed Abstract: 
  

Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages.

---

Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, CB2 OQH Cambridge, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.219 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.52	α = 90
b = 49.52	β = 90
c = 53.642	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-06-01 
• Released Date: 2016-07-20 
Deposition Author(s): Huguenin-Dezot, N., Chin, J.W.

---

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105181009
Medical Research Council (United Kingdom)	United Kingdom	UPA0241008

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2016-08-03
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence