3PG0

Crystal structure of designed 3-fold symmetric protein, ThreeFoil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein.

Broom, A.Doxey, A.C.Lobsanov, Y.D.Berthin, L.G.Rose, D.R.Howell, P.L.McConkey, B.J.Meiering, E.M.

(2012) Structure 20: 161-171

  • DOI: 10.1016/j.str.2011.10.021

  • PubMed Abstract: 
  • The high frequency of internal structural symmetry in common protein folds is presumed to reflect their evolutionary origins from the repetition and fusion of ancient peptide modules, but little is known about the primary sequence and physical determ ...

    The high frequency of internal structural symmetry in common protein folds is presumed to reflect their evolutionary origins from the repetition and fusion of ancient peptide modules, but little is known about the primary sequence and physical determinants of this process. Unexpectedly, a sequence and structural analysis of symmetric subdomain modules within an abundant and ancient globular fold, the β-trefoil, reveals that modular evolution is not simply a relic of the ancient past, but is an ongoing and recurring mechanism for regenerating symmetry, having occurred independently in numerous existing β-trefoil proteins. We performed a computational reconstruction of a β-trefoil subdomain module and repeated it to form a newly three-fold symmetric globular protein, ThreeFoil. In addition to its near perfect structural identity between symmetric modules, ThreeFoil is highly soluble, performs multivalent carbohydrate binding, and has remarkably high thermal stability. These findings have far-reaching implications for understanding the evolution and design of proteins via subdomain modules.


    Organizational Affiliation

    Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ThreeFoil
A
165N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

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Download CCD File 
A
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 45.012α = 90.00
b = 45.012β = 90.00
c = 113.439γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
BALBESphasing
d*TREKdata scaling
MOLREPphasing
CrystalCleardata collection
d*TREKdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description