6GD7 | pdb_00006gd7

Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.183 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Auto-regulated Protein Assembly on a Supramolecular Scaffold.

Rennie, M.L., Fox, G.C., Perez, J., Crowley, P.B.

(2018) Angew Chem Int Ed Engl 57: 13764-13769

  • DOI: https://doi.org/10.1002/anie.201807490
  • Primary Citation Related Structures: 
    6GD6, 6GD7, 6GD8, 6GD9

  • PubMed Abstract: 

    Controlled protein assembly provides a means to regulate function. Supramolecular building blocks, including rigid macrocycles, are versatile triggers of protein assembly. Now it is shown that sulfonato-calix[8]arene (sclx 8 ) mediates the formation of cytochrome c tetramers in solution. This tetramer spontaneously disassembles at ≥2 equivalents of sclx 8 , providing a remarkable example of auto-regulation. Using X-ray crystallography the sclx 8 binding sites on cytochrome c were characterized. Crystal structures at different protein-ligand ratios reveal varying degrees (up to 35 %) of protein surface coverage by the flexible calixarene and suggest a mechanism for oligomer disassembly. The solution structure of the oligomer was characterized by small-angle X-ray scattering. Overall, the data indicate calixarene-controlled protein assembly and disassembly without the requirement for a competitive inhibitor, and point to protein encapsulation by a flexible macrocycle.

    • Organizational Affiliation: 
    • School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.

Macromolecule Content 

  • Total Structure Weight: 14.24 kDa 
  • Atom Count: 1,247 
  • Modeled Residue Count: 108 
  • Deposited Residue Count: 108 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c iso-1108Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: CYC1, YJR048W, J1653
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.183 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.42α = 90
b = 81.42β = 90
c = 82.364γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/ERC/B2912 and 13/CDA/2168

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary