Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.22 kDa 
• Atom Count: 2424 
• Modelled Residue Count: 298 
• Deposited Residue Count: 304 
• Unique protein chains: 1

4S22

Crystal structure of K29 linked di-Ubiquitin

• DOI: 10.2210/pdb4S22/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2015-01-17 Released: 2015-04-08 
• Deposition Author(s): Kristariyanto, Y.A., Abdul Rehman, S.A., Campbell, D.G., Morrice, N.A., Johnson, C., Toth, R., Kulathu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin.

Kristariyanto, Y.A., Abdul Rehman, S.A., Campbell, D.G., Morrice, N.A., Johnson, C., Toth, R., Kulathu, Y.

(2015) Mol Cell 58: 83-94

• PubMed: 25752573 
• DOI: 10.1016/j.molcel.2015.01.041
• Primary Citation of Related Structures:  
  4S22, 4S1Z


• PubMed Abstract: 
  

Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages.

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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. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B, C, D	76	Bos taurus	Mutation(s): 0  Gene Names: UBA52, UBCEP2
Find proteins for P63048 (Bos taurus) Explore P63048  Go to UniProtKB:  P63048

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	A, B, D	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.45	α = 90
b = 69.245	β = 90.22
c = 60.055	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-17 
• Released Date: 2015-04-08 
Deposition Author(s): Kristariyanto, Y.A., Abdul Rehman, S.A., Campbell, D.G., Morrice, N.A., Johnson, C., Toth, R., Kulathu, Y.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references