4YC5

Beta1 synthetic solenoid protein

  • Classification: STRUCTURAL PROTEIN
  • Expression System: Escherichia coli

  • Deposited: 2015-02-19 Released: 2016-03-09 
  • Deposition Author(s): Murray, J.W.
  • Funding Organization(s): Biotechnology and Biological Sciences Research Council 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.

MacDonald, J.T.Kabasakal, B.V.Godding, D.Kraatz, S.Henderson, L.Barber, J.Freemont, P.S.Murray, J.W.

(2016) Proc.Natl.Acad.Sci.USA 113: 10346-10351

  • DOI: 10.1073/pnas.1525308113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemb ...

    The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops.


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; j.w.murray@imperial.ac.uk.,Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.,Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;,Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom;,Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta1
A
235N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.158 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.570α = 90.00
b = 64.570β = 90.00
c = 160.400γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-19 
  • Released Date: 2016-03-09 
  • Deposition Author(s): Murray, J.W.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/F023308/1

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations