6EIZ

A de novo designed hexameric coiled coil CC-Hex2 with farnesol bound in the channel.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

De Novo-Designed alpha-Helical Barrels as Receptors for Small Molecules.

Thomas, F.Dawson, W.M.Lang, E.J.M.Burton, A.J.Bartlett, G.J.Rhys, G.G.Mulholland, A.J.Woolfson, D.N.

(2018) ACS Synth Biol 7: 1808-1816

  • DOI: https://doi.org/10.1021/acssynbio.8b00225
  • Primary Citation of Related Structures:  
    6EIK, 6EIZ

  • PubMed Abstract: 

    We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.


  • Organizational Affiliation

    School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CC-Hex2
A, B, C, D, E
A, B, C, D, E, F
32synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FOF (Subject of Investigation/LOI)
Query on FOF

Download Ideal Coordinates CCD File 
G [auth F](2E,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-ol
C15 H26 O
CRDAMVZIKSXKFV-YFVJMOTDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.08α = 90
b = 126.23β = 90
c = 58.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2012- 536
European Research CouncilBelgium340764
Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research CouncilUnited KingdomBB/L01386X1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/G036764/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/K03927X/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 2.0: 2019-02-20
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 2.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Refinement description