6GD6

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

• PDB DOI: https://doi.org/10.2210/pdb6GD6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-04-23 Released: 2018-08-29 
• Deposition Author(s): Rennie, M.L., Fox, G.C., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.136 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 

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

• PubMed: 30109907 
• DOI: https://doi.org/10.1002/anie.201807490
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 14.63 kDa 
• Atom Count: 1,417 
• Modelled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c iso-1	A	108	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVB (Subject of Investigation/LOI)	C [auth A]	sulfonato-calix[8]arene C56 H48 O32 S8 KCEGJGDGMRAJEP-UHFFFAOYSA-N
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.136 
• R-Value Work: 0.119 
• R-Value Observed: 0.120 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.003	α = 90
b = 82.003	β = 90
c = 82.535	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Rennie, M.L., Fox, G.C., Crowley, P.B.

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Funding Organization	Location	Grant Number
Science Foundation Ireland	Ireland	13/ERC/B2912 and 13/CDA/2168

Revision History  

• 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