6G6H | pdb_00006g6h

Crystal structure of an antiparallel five-helix coiled coil 5H2L_2.1-I9L

• PDB DOI: https://doi.org/10.2210/pdb6G6H/pdb

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


• Deposited: 2018-04-01 Released: 2018-10-17 
• Deposition Author(s): Rhys, G.G., Brady, R.L., Woolfson, D.N.
• Funding Organization(s): Engineering and Physical Sciences Research Council, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Maintaining and breaking symmetry in homomeric coiled-coil assemblies.

Rhys, G.G., Wood, C.W., Lang, E.J.M., Mulholland, A.J., Brady, R.L., Thomson, A.R., Woolfson, D.N.

(2018) Nat Commun 9: 4132-4132

• PubMed: 30297707 
• DOI: https://doi.org/10.1038/s41467-018-06391-y
• Primary Citation Related Structures: 
  6G65, 6G66, 6G67, 6G68, 6G69, 6G6A, 6G6B, 6G6C, 6G6D, 6G6E, 6G6F, 6G6G, 6G6H


• PubMed Abstract: 
  

  In coiled-coil (CC) protein structures α-helices wrap around one another to form rope-like assemblies. Most natural and designed CCs have two-four helices and cyclic (C _n ) or dihedral (D _n ) symmetry. Increasingly, CCs with five or more helices are being reported. A subset of these higher-order CCs is of interest as they have accessible central channels that can be functionalised; they are α-helical barrels. These extended cavities are surprising given the drive to maximise buried hydrophobic surfaces during protein folding and assembly in water. Here, we show that α-helical barrels can be maintained by the strategic placement of β-branched aliphatic residues lining the lumen. Otherwise, the structures collapse or adjust to give more-complex multi-helix assemblies without C _n or D _n symmetry. Nonetheless, the structural hallmark of CCs-namely, knobs-into-holes packing of side chains between helices-is maintained leading to classes of CCs hitherto unobserved in nature or accessed by design.

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Organizational Affiliation: 
• School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail].
School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK.
Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.
School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK.
School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. [e-mail].
BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK. [e-mail].
School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 20.67 kDa 
• Atom Count: 1,614 
• Modeled Residue Count: 174 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5H2L_2.1-I9L	A, B, C, D, E	35	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.29	α = 90
b = 65.32	β = 90
c = 83.37	γ = 90

Software Package:

Software Name	Purpose
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
Arcimboldo	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Rhys, G.G., Brady, R.L., Woolfson, D.N.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/G036764/1
European Research Council	United Kingdom	340764

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Advisory, Data collection, Database references, Structure summary