4DZM

A de novo designed Coiled Coil CC-Di


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A basis set of de novo coiled-coil Peptide oligomers for rational protein design and synthetic biology.

Fletcher, J.M.Boyle, A.L.Bruning, M.Bartlett, G.J.Vincent, T.L.Zaccai, N.R.Armstrong, C.T.Bromley, E.H.Booth, P.J.Brady, R.L.Thomson, A.R.Woolfson, D.N.

(2012) ACS Synth Biol 1: 240-250

  • DOI: 10.1021/sb300028q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such com ...

    Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.


    Organizational Affiliation

    School of Chemistry, University of Bristol, Cantocks Close, Bristol BS8 1TS, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COILED-COIL PEPTIDE CC-DI
A, B
33N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PHI
Query on PHI
A, B
L-PEPTIDE LINKINGC9 H10 I N O2PHE
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.192 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 23.509α = 90.00
b = 23.509β = 90.00
c = 189.598γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SHELXSphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description, Source and taxonomy