6NAF | pdb_00006naf

De novo designed homo-trimeric amantadine-binding protein

• PDB DOI: https://doi.org/10.2210/pdb6NAF/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2018-12-05 Released: 2019-12-18 
• Deposition Author(s): Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.318 (Depositor) 
• R-Value Work: 
  0.277 (Depositor) 
• R-Value Observed: 
  0.280 (Depositor) 

Starting Model: experimental

Literature

De novo design of a homo-trimeric amantadine-binding protein.

Park, J., Selvaraj, B., McShan, A.C., Boyken, S.E., Wei, K.Y., Oberdorfer, G., DeGrado, W., Sgourakis, N.G., Cuneo, M.J., Myles, D.A., Baker, D.

(2019) Elife 8

• PubMed: 31854299 
• DOI: https://doi.org/10.7554/eLife.47839
• Primary Citation Related Structures: 
  6N9H, 6NAF


• PubMed Abstract: 
  

  The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C ₃ symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, United States.
Institute for Protein Design, University of Washington, Seattle, United States.
Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, United States.
Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States.
Department of Bioengineering, University of California, Berkeley, Berkeley, United States.
Institute of Biochemistry, Graz University of Technology, Graz, Austria.
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 9.31 kDa 
• Atom Count: 649 
• Modeled Residue Count: 74 
• Deposited Residue Count: 80 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amantadine-binding protein	A	80	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
308 (Subject of Investigation/LOI)	B [auth A]	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C10 H17 N DKNWSYNQZKUICI-CHIWXEEVSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.318 (Depositor) 
• R-Value Work:  0.277 (Depositor) 
• R-Value Observed: 0.280 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.61	α = 90
b = 50.61	β = 90
c = 68.82	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Selvaraj, B., Park, J., Cuneo, M.J., Myles, D.A.A., Baker, D.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description