4PNA

A de novo designed heptameric coiled coil CC-Hept

• PDB DOI: https://doi.org/10.2210/pdb4PNA/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-05-23 Released: 2014-10-22 
• Deposition Author(s): Burton, A.J., Wood, C.W., Thomson, A.R., Brady, R.L., Woolfson, D.N.
• Funding Organization(s): European Research Council, Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

Computational design of water-soluble alpha-helical barrels.

Thomson, A.R., Wood, C.W., Burton, A.J., Bartlett, G.J., Sessions, R.B., Brady, R.L., Woolfson, D.N.

(2014) Science 346: 485-488

• PubMed: 25342807 
• DOI: https://doi.org/10.1126/science.1257452
• Primary Citation of Related Structures:  
  4PN8, 4PN9, 4PNA, 4PNB, 4PND


• PubMed Abstract: 
  

  The design of protein sequences that fold into prescribed de novo structures is challenging. General solutions to this problem require geometric descriptions of protein folds and methods to fit sequences to these. The α-helical coiled coils present a promising class of protein for this and offer considerable scope for exploring hitherto unseen structures. For α-helical barrels, which have more than four helices and accessible central channels, many of the possible structures remain unobserved. Here, we combine geometrical considerations, knowledge-based scoring, and atomistic modeling to facilitate the design of new channel-containing α-helical barrels. X-ray crystal structures of the resulting designs match predicted in silico models. Furthermore, the observed channels are chemically defined and have diameters related to oligomer state, which present routes to design protein function.

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Organizational Affiliation: 

School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23.03 kDa 
• Atom Count: 1,704 
• Modelled Residue Count: 215 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CC-Hept	A, B, C, D, E, F, G	31	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth B], I [auth F], J [auth G], K [auth G]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.53	α = 90
b = 48.74	β = 90
c = 129.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Burton, A.J., Wood, C.W., Thomson, A.R., Brady, R.L., Woolfson, D.N.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	340764
Engineering and Physical Sciences Research Council	United Kingdom	EP/J001430/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J008990/1

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references
• Version 2.0: 2017-08-30
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2017-09-13
  Changes: Author supporting evidence