3TEU

Crystal structure of fibcon

• PDB DOI: https://doi.org/10.2210/pdb3TEU/pdb

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


• Deposited: 2011-08-15 Released: 2012-05-16 
• Deposition Author(s): Luo, J., Jacobs, S., Teplyakov, A., Obmolova, G., O'Neil, K., Gilliland, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 

Starting Model: experimental

Literature

Design of novel FN3 domains with high stability by a consensus sequence approach.

Jacobs, S.A., Diem, M.D., Luo, J., Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L., O'Neil, K.T.

(2012) Protein Eng Des Sel 25: 107-117

• PubMed: 22240293 
• DOI: https://doi.org/10.1093/protein/gzr064
• Primary Citation of Related Structures:  
  3TES, 3TEU


• PubMed Abstract: 
  

  The use of consensus design to produce stable proteins has been applied to numerous structures and classes of proteins. Here, we describe the engineering of novel FN3 domains from two different proteins, namely human fibronectin and human tenascin-C, as potential alternative scaffold biotherapeutics. The resulting FN3 domains were found to be robustly expressed in Escherichia coli, soluble and highly stable, with melting temperatures of 89 and 78°C, respectively. X-ray crystallography was used to confirm that the consensus approach led to a structure consistent with the FN3 design despite having only low-sequence identity to natural FN3 domains. The ability of the Tenascin consensus domain to withstand mutations in the loop regions connecting the β-strands was investigated using alanine scanning mutagenesis demonstrating the potential for randomization in these regions. Finally, rational design was used to produce point mutations that significantly increase the stability of one of the consensus domains. Together our data suggest that consensus FN3 domains have potential utility as alternative scaffold therapeutics.

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Organizational Affiliation: 

Janssen Research & Development, L.L.C., Radnor, PA 19087, USA. [e-mail]

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: 10.49 kDa 
• Atom Count: 969 
• Modelled Residue Count: 98 
• Deposited Residue Count: 98 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibcon	A	98	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	B [auth A]	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.139 
• R-Value Work: 0.111 
• R-Value Observed: 0.112 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.39	α = 90
b = 40.07	β = 90
c = 61.52	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Luo, J., Jacobs, S., Teplyakov, A., Obmolova, G., O'Neil, K., Gilliland, G.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description