7BBT

Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG pseudorotaxane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Noncovalent Protein-Pseudorotaxane Assembly Incorporating an Extended Arm Calix[8]arene with alpha-Helical Recognition Properties.

Mockler, N.M.Ramberg, K.O.Guagnini, F.Raston, C.L.Crowley, P.B.

(2021) Cryst Growth Des 21: 1424-1427

  • DOI: https://doi.org/10.1021/acs.cgd.0c01717
  • Primary Citation of Related Structures:  
    7BBT

  • PubMed Abstract: 

    Water-soluble, anionic calix[ n ]arenes are useful receptors for protein recognition and assembly. For example, sulfonato-calix[8]arene ( sclx 8 ) can encapsulate proteins and direct their assembly into porous frameworks. In this work, we turned our attention to an "extended arm" calixarene with 16 phenyl rings. We hypothesized that this larger receptor would have increased capacity for protein masking/encapsulation. A cocrystal structure of p -benzyl-sulfonato-calix[8]arene ( b-sclx 8 ) and cytochrome c (cyt c ) revealed a surprising assembly. A pseudorotaxane comprising a stack of three b-sclx 8 molecules threaded by polyethylene glycol (PEG) was bound to the protein. The trimeric b-sclx 8 stack, a tubelike structure with a highly charged surface, mediated assembly via a new mode of protein recognition. The calixarene stack presents four hydrophobic grooves, each of which binds to one cyt c by accommodating the N-terminal α-helix. This unprecedented binding mode suggests new possibilities for supramolecular protein chemistry.


  • Organizational Affiliation

    School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1
A, B, C, D
108Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: CYC1YJR048WJ1653
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T8W (Subject of Investigation/LOI)
Query on T8W

Download Ideal Coordinates CCD File 
H [auth C],
I [auth C],
K [auth D]
4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35,41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133,37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55),15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51),39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate
C112 H88 O32 S8
MTYKCVHEIUYKCZ-UHFFFAOYSA-F
15P (Subject of Investigation/LOI)
Query on 15P

Download Ideal Coordinates CCD File 
L [auth D]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
J [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.851α = 90
b = 70.215β = 102.93
c = 70.175γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland13/CDA/2168
Irish Research CouncilIrelandGOIPD/2019/513

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary