Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 10.47 kDa 
• Atom Count: 813 
• Residue Count: 96 
• Unique protein chains: 1

1G6U

CRYSTAL STRUCTURE OF A DOMAIN SWAPPED DIMER

• DOI: 10.2210/pdb1G6U/pdb

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2000-11-07 Released: 2001-02-21 
• Deposition Author(s): Ogihara, N.L., Ghirlanda, G., Bryson, J.W., Gingery, M., DeGrado, W.F., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Design of three-dimensional domain-swapped dimers and fibrous oligomers.

Ogihara, N.L., Ghirlanda, G., Bryson, J.W., Gingery, M., DeGrado, W.F., Eisenberg, D.

(2001) Proc Natl Acad Sci U S A 98: 1404-1409

• PubMed: 11171963 
• DOI: 10.1073/pnas.98.4.1404
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Three-dimensional (3D) domain-swapped proteins are intermolecularly folded analogs of monomeric proteins; both are stabilized by the identical interactions, but the individual domains interact intramolecularly in monomeric proteins, whereas they form intermolecular interactions in 3D domain-swapped structures. The structures and conditions of formation of several domain-swapped dimers and trimers are known, but the formation of higher order 3D domain-swapped oligomers has been less thoroughly studied. Here we contrast the structural consequences of domain swapping from two designed three-helix bundles: one with an up-down-up topology, and the other with an up-down-down topology. The up-down-up topology gives rise to a domain-swapped dimer whose structure has been determined to 1.5 A resolution by x-ray crystallography. In contrast, the domain-swapped protein with an up-down-down topology forms fibrils as shown by electron microscopy and dynamic light scattering. This demonstrates that design principles can predict the oligomeric state of 3D domain-swapped molecules, which should aid in the design of domain-swapped proteins and biomaterials.

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Organizational Affiliation: 

UCLA-DOE Laboratory of Structural Biology and the Department of Chemistry and Biochemistry, P.O. Box 951570, University of California, Los Angeles, CA 90095-1570, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DOMAIN SWAPPED DIMER	A, B	48	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	B	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.04	α = 90
b = 64.04	β = 90
c = 64.04	γ = 90

Software Package:

Software Name	Purpose
DM	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-11-07 
• Released Date: 2001-02-21 
Deposition Author(s): Ogihara, N.L., Ghirlanda, G., Bryson, J.W., Gingery, M., DeGrado, W.F., Eisenberg, D.

Revision History 

• Version 1.0: 2001-02-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance