8UGC

FD15: Flat repeat helix-turn-helix-turn protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.492 
  • R-Value Work: 0.465 
  • R-Value Observed: 0.466 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Directing polymorph specific calcium carbonate formation with de novo protein templates.

Davila-Hernandez, F.A.Jin, B.Pyles, H.Zhang, S.Wang, Z.Huddy, T.F.Bera, A.K.Kang, A.Chen, C.L.De Yoreo, J.J.Baker, D.

(2023) Nat Commun 14: 8191-8191

  • DOI: https://doi.org/10.1038/s41467-023-43608-1
  • Primary Citation of Related Structures:  
    8UGC

  • PubMed Abstract: 

    Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-Ca 2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FD15
A, B
393synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.492 
  • R-Value Work: 0.465 
  • R-Value Observed: 0.466 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.666α = 90
b = 122.784β = 97.61
c = 89.995γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release