Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 22665.72 
• Atom Count: 1567 
• Residue Count: 189 
• Unique protein chains: 1

3Q3F

Engineering Domain-Swapped Binding Interfaces by Mutually Exclusive Folding: Insertion of Ubiquitin into position 103 of Barnase

• DOI: 10.2210/pdb3Q3F/pdb

• Classification: HYDROLASE PROTEIN BINDING
• Organism(s): Bacillus amyloliquefaciens, Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2010-12-21 Released: 2012-01-25 
• Deposition Author(s): Ha, J.-H., Karchin, J.M., Walker-Kopp, N., Huang, L.-S., Berry, E.A., Loh, S.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.169 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 

Literature

Engineering domain-swapped binding interfaces by mutually exclusive folding.

Ha, J.H., Karchin, J.M., Walker-Kopp, N., Huang, L.S., Berry, E.A., Loh, S.N.

(2012) J.Mol.Biol. 416: 495-502

• PubMed: 22245575 
• DOI: 10.1016/j.jmb.2011.12.050


• PubMed Abstract: 
  

Domain swapping is a mechanism for forming protein dimers and oligomers with high specificity. It is distinct from other forms of oligomerization in that the binding interface is formed by reciprocal exchange of polypeptide segments. Swapping plays a physiological role in protein-protein recognition, and it can also potentially be exploited as a mechanism for controlled self-assembly. Here, we demonstrate that domain-swapped interfaces can be engineered by inserting one protein into a surface loop of another protein. The key to facilitating a domain swap is to destabilize the protein when it is monomeric but not when it is oligomeric. We achieve this condition by employing the "mutually exclusive folding" design to apply conformational stress to the monomeric state. Ubiquitin (Ub) is inserted into one of six surface loops of barnase (Bn). The 38-Å amino-to-carboxy-terminal distance of Ub stresses the Bn monomer, causing it to split at the point of insertion. The 2.2-Å X-ray structure of one insertion variant reveals that strain is relieved by intermolecular folding with an identically unfolded Bn domain, resulting in a domain-swapped polymer. All six constructs oligomerize, suggesting that inserting Ub into each surface loop of Bn results in a similar domain-swapping event. Binding affinity can be tuned by varying the length of the peptide linkers used to join the two proteins, which modulates the extent of stress. Engineered, swapped proteins have the potential to be used to fabricate "smart" biomaterials, or as binding modules from which to assemble heterologous, multi-subunit protein complexes.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonuclease/Ubiquitin chimeric protein	A	189	Bacillus amyloliquefaciens, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: UBC EC: 3.1.27.-
Find proteins for P00648 (Bacillus amyloliquefaciens) Go to UniProtKB:  P00648
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.169 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 86.872	α = 90.00
b = 86.872	β = 90.00
c = 75.571	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
Adxv	data processing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-21 
• Released Date: 2012-01-25 
• Deposition Author(s): Ha, J.-H., Karchin, J.M., Walker-Kopp, N., Huang, L.-S., Berry, E.A., Loh, S.N.

Revision History 

• Version 1.0: 2012-01-25
  Type: Initial release
• Version 1.1: 2012-02-01
  Type: Database references
• Version 1.2: 2012-03-07
  Type: Database references
• Version 1.3: 2017-07-26
  Type: Refinement description, Source and taxonomy
• Version 1.4: 2017-11-08
  Type: Refinement description