9Q1V | pdb_00009q1v

Crystal Structure of de novo design FimH minibinder F7 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

De Novo Design of Miniprotein Inhibitors of Bacterial Adhesins.

Chazin-Gray, A.M.Thompson, T.R.Lopatto, E.D.B.Magala, P.Erickson, P.W.Hunt, A.C.Manchenko, A.Aprikian, P.Tchesnokova, V.Basova, I.Sanick, D.A.Tamadonfar, K.O.Timm, M.R.Pinkner, J.S.Dodson, K.W.Kang, A.Joyce, E.Bera, A.K.Schmitz, A.J.Ellebedy, A.H.Hvorecny, K.L.Cartwright, M.J.Vernet, A.Bardales, S.White, D.Klevit, R.E.Sokurenko, E.V.Hultgren, S.J.Baker, D.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.08.18.670751
  • Primary Citation of Related Structures:  
    9Q1H, 9Q1V

  • PubMed Abstract: 

    The rise of multidrug-resistant bacterial infections necessitates the discovery of novel antimicrobial strategies. Here, we show that protein design provides a generalizable means of generating new antimicrobials by neutralizing the function of bacterial adhesins, which are virulence factors critical in host-pathogen interactions. We de novo designed high-affinity miniprotein binders to FimH and Abp1D/Abp2D chaperone usher pili adhesins from uropathogenic Escherichia coli and Acinetobacter baumannii , respectively, which are implicated in mediating both uncomplicated and catheter-associated urinary tract infections (UTI) responsible for significant morbidity and mortality worldwide. The designed antagonists have high specificity and stability, disrupt bacterial recognition of host receptors, block biofilm formation, and are effective in treating and preventing uncomplicated and catheter-associated UTIs in vivo . Targeting virulence factors outside the cell membrane with protein design provides a rapid route to next-generation therapeutics that can disrupt pathogenesis and thus are capable of treating and preventing disease in an antibiotic-sparing manner.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FimH minibinder F7
A, C
68synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesin
B, D
165Escherichia coliMutation(s): 4 
Gene Names: fimHb4320JW4283
UniProt
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08191
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.263 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.967α = 90
b = 52.387β = 101.795
c = 72.865γ = 90
Software Package:
Software NamePurpose
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--
Defense Advanced Research Projects Agency (DARPA)United StatesHR0011-21-2- 0012

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release