9NJY | pdb_00009njy

Terminal two domains of ClfA002 with bound Fab of AZD7745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.219 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.209 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of ClfA002 in Complex With Neutralizing Antibody AZD7745 Provides Insight into Its Broad Neutralization Mechanism in Staphylococcus aureus Infection.

Tkaczyk, C.Keren-Kaplan, T.Gamson, A.Warrener, P.Semenova, E.Rosenthal, K.Barnes, A.Ahani, B.Sellman, B.R.Podlaha, O.Oganesyan, V.

(2025) J Infect Dis 232: e421-e430

  • DOI: https://doi.org/10.1093/infdis/jiaf357
  • Primary Citation of Related Structures:  
    9NJY

  • PubMed Abstract: 

    Complications due to Staphylococcus aureus infections are a major health concern as current therapies lack broad coverage; therefore, development of a broad neutralizing therapy is critical. We previously showed that a mAb combination comprising suvratoxumab and AZD7745 targeting respectively alpha toxin and clumping factor A (ClfA), two S. aureus virulence factors, provided broad strain coverage in a mouse model. To understand the basis for the broad strain coverage of AZD7745 the epitope was determined. Moreover, we surveyed a global collection of bacteremia isolates to study AZD7745 epitope conservation and neutralizing activity. AZD7745 epitope was determined from the cocrystal structure of AZD7745 Fab with the N2N3 fibrinogen binding domain of ClfA (at 1.58Å). A geographically diverse collection of 174 S. aureus bacteremia isolates was collected between 2022-2023. Whole genome sequencing was performed to determine the presence of the clfA gene and AZD7745 epitope conservation. AZD7745 neutralizing activity was tested in-vitro against a representative strain of each ClfA variant in a fibrinogen/ClfA binding assay. The AZD7745 epitope contains 12 binding residues on the ClfA N3 domain. Among the 174 isolates, we identified 45 ClfA subtypes with 29 presenting amino-acid variations on contact residues. Nonetheless, AZD7745 exhibited neutralizing activity against each subtype. We showed that AZD7745 binding to ClfA N3 domain imposes a conformational change which prevents fibrinogen binding to ClfA. ClfA is ubiquitously present on S. aureus global clinical isolates, and AZD7745 epitope is highly conserved. This suggests that AZD7745 can confer broad coverage against S. aureus.


  • Organizational Affiliation
    • Vaccines and Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD 20878, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Clumping factor A302Staphylococcus aureusMutation(s): 0 
Gene Names: clfASA0742
UniProt
Find proteins for Q99VJ4 (Staphylococcus aureus (strain N315))
Explore Q99VJ4 
Go to UniProtKB:  Q99VJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99VJ4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody, heavy chain fragment, antigen bindingB [auth H]225MammaliaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Human antibody, light chain, antigen bindingC [auth L]214MammaliaMutation(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: 1.58 Å
  • R-Value Free:  0.219 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.209 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.582α = 90
b = 66.164β = 90.583
c = 107.875γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references