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PDBsum entry 3o4a

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protein ligands Protein-protein interface(s) links
De novo protein PDB id
3o4a
Jmol
Contents
Protein chains
123 a.a. *
Ligands
TRS ×4
SO4 ×10
Waters ×624
* Residue conservation analysis
PDB id:
3o4a
Name: De novo protein
Title: Crystal structure of symfoil-2: de novo designed beta-trefoi architecture with symmetric primary structure
Structure: De novo designed beta-trefoil architecture with s primary structure. Chain: a, b, c, d. Engineered: yes
Source: Synthetic construct. Artificial gene. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.45Å     R-factor:   0.187     R-free:   0.215
Authors: J.Lee,M.Blaber
Key ref: J.Lee and M.Blaber (2011). Experimental support for the evolution of symmetric protein architecture from a simple peptide motif. Proc Natl Acad Sci U S A, 108, 126-130. PubMed id: 21173271
Date:
26-Jul-10     Release date:   22-Dec-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 123 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     fibroblast growth factor receptor signaling pathway   1 term 
  Biochemical function     fibroblast growth factor receptor binding     2 terms  

 

 
Proc Natl Acad Sci U S A 108:126-130 (2011)
PubMed id: 21173271  
 
 
Experimental support for the evolution of symmetric protein architecture from a simple peptide motif.
J.Lee, M.Blaber.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315087 J.Lee, S.I.Blaber, V.K.Dubey, and M.Blaber (2011).
A polypeptide "building block" for the β-trefoil fold identified by "top-down symmetric deconstruction".
  J Mol Biol, 407, 744-763.
PDB code: 3o3q
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