5ET3

Crystal Structure of De novo Designed Fullerene organizing peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Protein-directed self-assembly of a fullerene crystal.

Kim, K.-H.Ko, D.-K.Kim, Y.-T.Kim, N.H.Paul, J.Zhang, S.-Q.Murray, C.B.Acharya, R.DeGrado, W.F.Kim, Y.H.Grigoryan, G.

(2016) Nat Commun 7: 11429-11429

  • DOI: https://doi.org/10.1038/ncomms11429
  • Primary Citation of Related Structures:  
    5ET3, 5HKN, 5HKR

  • PubMed Abstract: 

    Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.


  • Organizational Affiliation

    SKKU Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon 16419, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fullerene Organizing Protein (C60Sol-COP-3)
A, B
30synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
60C
Query on 60C

Download Ideal Coordinates CCD File 
C [auth A](C_{60}-I_{h})[5,6]fullerene
C60
XMWRBQBLMFGWIX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.145α = 90
b = 42.145β = 90
c = 66.787γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic OfNRF-2014R1A1A2055647

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description