Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 13.92 kDa 
• Atom Count: 1025 
• Residue Count: 124 
• Unique protein chains: 2

4UN2

Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin

• DOI: 10.2210/pdb4UN2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-23 Released: 2014-08-27 
• Deposition Author(s): Michielssens, S., Peters, J.H., Ban, D., Pratihar, S., Seeliger, D., Sharma, M., Giller, K., Sabo, T.M., Becker, S., Lee, D., Griesinger, C., de Groot, B.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.196 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

A Designed Conformational Shift to Control Protein Binding Specificity.

Michielssens, S., Peters, J.H., Ban, D., Pratihar, S., Seeliger, D., Sharma, M., Giller, K., Sabo, T.M., Becker, S., Lee, D., Griesinger, C., De Groot, B.L.

(2014) Angew Chem Int Ed Engl 53: 10367

• PubMed: 25115701 
• DOI: 10.1002/anie.201403102
• Primary Citation of Related Structures:  
  4UN2


• PubMed Abstract: 
  

In a conformational selection scenario, manipulating the populations of binding-competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground-state ensemble between open and closed substates that have a similar population in the wild-type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin's binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding-competent substates.

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Organizational Affiliation: 

Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen (Germany) http://www.mpibpc.mpg.de/groups/de_groot/

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN DOMAIN-CONTAINING PROTEIN DSK2	B	48	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P48510 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48510  Go to UniProtKB:  P48510

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.196 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.971	α = 90
b = 77.972	β = 90
c = 49.485	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-23 
• Released Date: 2014-08-27 
Deposition Author(s): Michielssens, S., Peters, J.H., Ban, D., Pratihar, S., Seeliger, D., Sharma, M., Giller, K., Sabo, T.M., Becker, S., Lee, D., Griesinger, C., de Groot, B.L.

Revision History 

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references