Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.83 kDa 
• Atom Count: 657 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

4Y1H

Crystal structure of K33 linked tri-Ubiquitin

• PDB DOI: 10.2210/pdb4Y1H/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2015-02-07 Released: 2015-03-18 
• Deposition Author(s): Kristariyanto, Y.A., Abdul Rehman, S.A., Choi, S.Y., Ritorto, S., Campbell, D.G., Morrice, N.A., Toth, R., Kulathu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.194 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Assembly and structure of Lys33-linked polyubiquitin reveals distinct conformations.

Kristariyanto, Y.A., Choi, S.Y., Rehman, S.A., Ritorto, M.S., Campbell, D.G., Morrice, N.A., Toth, R., Kulathu, Y.

(2015) Biochem J 467: 345-352

• PubMed: 25723849 
• DOI: 10.1042/BJ20141502
• Primary Citation of Related Structures:  
  4XYZ, 4Y1H


• PubMed Abstract: 
  

Ubiquitylation regulates a multitude of biological processes and this versatility stems from the ability of ubiquitin (Ub) to form topologically different polymers of eight different linkage types. Whereas some linkages have been studied in detail, other linkage types including Lys33-linked polyUb are poorly understood. In the present study, we identify an enzymatic system for the large-scale assembly of Lys33 chains by combining the HECT (homologous to the E6-AP C-terminus) E3 ligase AREL1 (apoptosis-resistant E3 Ub protein ligase 1) with linkage selective deubiquitinases (DUBs). Moreover, this first characterization of the chain selectivity of AREL1 indicates its preference for assembling Lys33- and Lys11-linked Ub chains. Intriguingly, the crystal structure of Lys33-linked diUb reveals that it adopts a compact conformation very similar to that observed for Lys11-linked diUb. In contrast, crystallographic analysis of Lys33-linked triUb reveals a more extended conformation. These two distinct conformational states of Lys33-linked polyUb may be selectively recognized by Ub-binding domains (UBD) and enzymes of the Ub system. Importantly, our work provides a method to assemble Lys33-linked polyUb that will allow further characterization of this atypical chain type.

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Organizational Affiliation: 

*MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S27a	A	76	Bos taurus	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt
Find proteins for P62992 (Bos taurus) Explore P62992  Go to UniProtKB:  P62992

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.194 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.938	α = 90
b = 41.831	β = 90
c = 47.602	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-02-07 
• Released Date: 2015-03-18 
Deposition Author(s): Kristariyanto, Y.A., Abdul Rehman, S.A., Choi, S.Y., Ritorto, S., Campbell, D.G., Morrice, N.A., Toth, R., Kulathu, Y.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Derived calculations