3O49 | pdb_00003o49

Crystal structure of Symfoil-1: de novo designed beta-trefoil architecture with symmetric primary structure

• PDB DOI: https://doi.org/10.2210/pdb3O49/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-26 Released: 2010-12-22 
• Deposition Author(s): Lee, J., Blaber, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.227 (Depositor) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Experimental support for the evolution of symmetric protein architecture from a simple peptide motif.

Lee, J., Blaber, M.

(2011) Proc Natl Acad Sci U S A 108: 126-130

• PubMed: 21173271 
• DOI: https://doi.org/10.1073/pnas.1015032108
• Primary Citation Related Structures: 
  3O49, 3O4A, 3O4B, 3O4C, 3O4D, 3OGF, 3OL0


• PubMed Abstract: 
  

  The majority of protein architectures exhibit elements of structural symmetry, and "gene duplication and fusion" is the evolutionary mechanism generally hypothesized to be responsible for their emergence from simple peptide motifs. Despite the central importance of the gene duplication and fusion hypothesis, experimental support for a plausible evolutionary pathway for a specific protein architecture has yet to be effectively demonstrated. To address this question, a unique "top-down symmetric deconstruction" strategy was utilized to successfully identify a simple peptide motif capable of recapitulating, via gene duplication and fusion processes, a symmetric protein architecture (the threefold symmetric β-trefoil fold). The folding properties of intermediary forms in this deconstruction agree precisely with a previously proposed "conserved architecture" model for symmetric protein evolution. Furthermore, a route through foldable sequence-space between the simple peptide motif and extant protein fold is demonstrated. These results provide compelling experimental support for a plausible evolutionary pathway of symmetric protein architecture via gene duplication and fusion processes.

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Organizational Affiliation: 
• Department of Biomedical Sciences, Florida State University, Tallahassee FL 32306-4300, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 15.96 kDa 
• Atom Count: 1,163 
• Modeled Residue Count: 123 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
de novo designed beta-trefoil architecture with symmetric primary structure	A	142	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.227 (Depositor) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.365	α = 90
b = 53.351	β = 90
c = 85.175	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Lee, J., Blaber, M.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations