Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene

Experimental Data Snapshot

  • Resolution: 2.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Calixarene capture of partially unfolded cytochrome c.

Engilberge, S.Rennie, M.L.Crowley, P.B.

(2019) FEBS Lett 593: 2112-2117

  • DOI: https://doi.org/10.1002/1873-3468.13512
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Supramolecular receptors such as water-soluble calixarenes are in development as 'molecular glues' for protein assembly. Here, we obtained cocrystals of sulfonato-calix[6]arene (sclx 6 ) and yeast cytochrome c (cytc) in the presence of imidazole. A crystal structure at 2.65 Å resolution reveals major structural rearrangement and disorder in imidazole-bound cytc. The largest protein-calixarene interface involves 440 Å 2 of the protein surface with key contacts at Arg13, Lys73, and Lys79. These lysines participate in alkaline transitions of cytc and are part of Ω-loop D, which is substantially restructured in the complex with sclx 6 . The structural modification also includes Ω-loop C, which is disordered (residues 41-55 inclusive). These results suggest the possibility of using supramolecular scaffolds to trap partially disordered proteins.

  • Organizational Affiliation

    School of Chemistry, National University of Ireland Galway, Galway, Ireland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1108Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: CYC1YJR048WJ1653
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.762α = 90
b = 74.762β = 90
c = 60.033γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description