6RGI | pdb_00006rgi

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

• PDB DOI: https://doi.org/10.2210/pdb6RGI/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-04-16 Released: 2019-07-10 
• Deposition Author(s): Engilberge, S., Rennie, M.L., Crowley, P.B.
• Funding Organization(s): Science Foundation Ireland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Calixarene capture of partially unfolded cytochrome c.

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

(2019) FEBS Lett 593: 2112-2117

• PubMed: 31254353 
• DOI: https://doi.org/10.1002/1873-3468.13512
• Primary Citation Related Structures: 
  6RGI


• 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.

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

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.84 kDa 
• Atom Count: 867 
• Modeled Residue Count: 92 
• 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
FWQ	C [auth A]	p-sulfonatocalix[6]arene C42 H30 O24 S6 BXOUPTJVBGEDIR-UHFFFAOYSA-H
HEC	B [auth A]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.250 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.762	α = 90
b = 74.762	β = 90
c = 60.033	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Engilberge, S., Rennie, M.L., Crowley, P.B.

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

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Structure summary