9BQW | pdb_00009bqw

Fab F945-DbpA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Models: experimental
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This is version 1.0 of the entry. See complete history


Literature

Germline encoded residues dominate the interaction of a human monoclonal antibody with decorin binding protein A of Borrelia burgdorferi.

Rudolph, M.J.Muriuki, B.M.Chen, Y.Vance, D.J.Vorauer, C.Piazza, C.L.Freeman-Gallant, G.Golonka, R.M.Mirabile, G.Guttman, M.Cavacini, L.A.Mantis, N.J.

(2025) Front Immunol 16: 1611828-1611828

  • DOI: https://doi.org/10.3389/fimmu.2025.1611828
  • Primary Citation of Related Structures:  
    9BQW

  • PubMed Abstract: 

    During the course of Lyme disease, humans mount a robust and sustained antibody response against dozens of Borrelia burgdorferi outer surface lipoproteins. Identifying which antibodies are associated with spirochete clearance and disease resolution is of paramount importance in therapeutic development. In this study, we describe the isolation and structural characterization of a human monoclonal antibody (MAb) against decorin binding protein A (DbpA), one of the most immunogenic of B. burgdorferi 's outer surface proteins. High-resolution epitope mapping by HDX-MS and X-ray crystallography revealed that F945 associates with a lateral face of DbpA in a side-on orientation without obstructing resides associated with DbpA's ability to bind components of the extracellular matrix. The structure of the DbpA-F945 Fab complex revealed an outsized role for variable light chain (V L ) germline encoded residues in mediating DbpA interactions. In fact, the majority of the critical contacts between F945 and DbpA involved V k 1-33 germline encoded residues, suggesting that certain human B cell receptors (BCR) may be preconfigured to recognize DbpA and therefore have a lower threshold for B cell activation and clonal development. Passive administration of F945 IgG was not sufficient to protect against B. burgdorferi in a mouse model of needle infection, although these experiments do not rule out a role for F945 in influencing B. burgdorferi tissue tropism and/or retention within specific niches. Nonetheless, it is tempting to speculate that F945 represents a class of DbpA antibodies with value in Lyme disease diagnostics, but that may not contribute to B. burgdorferi clearance or disease resolution in humans.


  • Organizational Affiliation
    • New York Structural Biology Center, New York, NY, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decorin-binding protein A163Borreliella burgdorferi B31Mutation(s): 0 
Gene Names: dbpABB_A24
UniProt
Find proteins for O50917 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31))
Explore O50917 
Go to UniProtKB:  O50917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50917
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F945 Fab Heavy ChainB [auth H]228Homo sapiensMutation(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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
F945 Fab Light ChainC [auth L]213Homo sapiensMutation(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: 2.55 Å
  • R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.105α = 90
b = 86.461β = 90
c = 151.484γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93019C00040

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release