Zn-Bound Structure of Computationally Designed Homotrimer Tet4

Experimental Data Snapshot

  • Resolution: 2.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 

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Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries.

Hoffnagle, A.M.Tezcan, F.A.

(2023) J Am Chem Soc 145: 14208-14214

  • DOI: https://doi.org/10.1021/jacs.3c04047
  • Primary Citation of Related Structures:  
    8SJF, 8SJG, 8SJH, 8SJI

  • PubMed Abstract: 

    We report a new computational protein design method for the construction of oligomeric protein assemblies around metal centers with predefined coordination geometries. We apply this method to design two homotrimeric assemblies, Tet4 and TP1, with tetrahedral and trigonal-pyramidal tris(histidine) metal coordination geometries, respectively, and demonstrate that both assemblies form the targeted metal centers with ≤0.2 Å accuracy. Although Tet4 and TP1 are constructed from the same parent protein building block, they are distinct in terms of their overall architectures, the environment surrounding the metal centers, and their metal-based reactivities, illustrating the versatility of our approach.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
114synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.245 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.663α = 90
b = 67.663β = 90
c = 109.635γ = 120
Software Package:
Software NamePurpose
APEXdata reduction
APEXdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM138884

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references