Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.75 kDa 
• Atom Count: 1,874 
• Modelled Residue Count: 215 
• Deposited Residue Count: 235 
• Unique protein chains: 1

 4YC5

Beta1 synthetic solenoid protein

• PDB DOI: 10.2210/pdb4YC5/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

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 U S A 113: 10346-10351

• PubMed: 27573845 
• DOI: 10.1073/pnas.1525308113
• Primary Citation of Related Structures:  
  4YC5, 4YCQ, 4YDT, 4YEI, 4YFO, 5DI5, 5DN0, 5DNS, 5DQA, 5DRA, 5DZB


• 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-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.

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Organizational Affiliation: 

Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta1	A	235	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.57	α = 90
b = 64.57	β = 90
c = 160.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/F023308/1

Revision History  

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