5HKR | pdb_00005hkr

Crystal structure of de novo designed fullerene organising protein complex with fullerene

• PDB DOI: https://doi.org/10.2210/pdb5HKR/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2016-01-14 Released: 2016-05-04 
• Deposition Author(s): Acharya, R., Kim, Y.H., Grigoryan, G., DeGardo, W.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

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

• PubMed: 27113637 
• DOI: https://doi.org/10.1038/ncomms11429
• Primary Citation 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.
Department of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.
School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha 752050, India.
Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, USA.
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Department of Chemistry and Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon 16419, Korea.
Department of Computer Science and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 7.1 kDa 
• Atom Count: 512 
• Modeled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fullerene organizing protein	A, B	30	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
60C	C [auth B]	(C_{60}-I_{h})[5,6]fullerene C60 XMWRBQBLMFGWIX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.713	α = 90
b = 41.713	β = 90
c = 66.808	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Acharya, R., Kim, Y.H., Grigoryan, G., DeGardo, W.F.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references