6BE2

Crystal structure of a polysaccharide-binding human Fab (F598)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for antibody targeting of the broadly expressed microbial polysaccharide poly-N-acetylglucosamine.

Soliman, C.Walduck, A.K.Yuriev, E.Richards, J.S.Cywes-Bentley, C.Pier, G.B.Ramsland, P.A.

(2018) J. Biol. Chem. 293: 5079-5089

  • DOI: 10.1074/jbc.RA117.001170
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In response to the widespread emergence of antibiotic-resistant microbes, new therapeutic agents are required for many human pathogens. A non-mammalian polysaccharide, poly- <i>N </i>-acetyl-d-glucosamine (PNAG), is produced by bacteria, fungi, and p ...

    In response to the widespread emergence of antibiotic-resistant microbes, new therapeutic agents are required for many human pathogens. A non-mammalian polysaccharide, poly- N -acetyl-d-glucosamine (PNAG), is produced by bacteria, fungi, and protozoan parasites. Antibodies that bind to PNAG and its deacetylated form (dPNAG) exhibit promising in vitro and in vivo activities against many microbes. A human IgG1 mAb (F598) that binds both PNAG and dPNAG has opsonic and protective activities against multiple microbial pathogens and is undergoing preclinical and clinical assessments as a broad-spectrum antimicrobial therapy. Here, to understand how F598 targets PNAG, we determined crystal structures of the unliganded F598 antigen-binding fragment (Fab) and its complexes with N -acetyl-d-glucosamine (GlcNAc) and a PNAG oligosaccharide. We found that F598 recognizes PNAG through a large groove-shaped binding site that traverses the entire light- and heavy-chain interface and accommodates at least five GlcNAc residues. The Fab-GlcNAc complex revealed a deep binding pocket in which the monosaccharide and a core GlcNAc of the oligosaccharide were almost identically positioned, suggesting an anchored binding mechanism of PNAG by F598. The Fab used in our structural analyses retained binding to PNAG on the surface of an antibiotic-resistant, biofilm-forming strain of Staphylococcus aureus Additionally, a model of intact F598 binding to two pentasaccharide epitopes indicates that the Fab arms can span at least 40 GlcNAc residues on an extended PNAG chain. Our findings unravel the structural basis for F598 binding to PNAG on microbial surfaces and biofilms.


    Organizational Affiliation

    From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia, paul.ramsland@rmit.edu.au.,Department of Immunology, Central Clinical School, Monash University, Victoria 3004, Melbourne, Australia, and.,Department of Infectious Diseases, Central Clinical School, Alfred Hospital, Melbourne, Victoria 3004, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria 3052, Australia.,Disease Elimination Program, Burnet Institute, Melbourne, Victoria 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Victoria 3084.,Department of Medicine, University of Melbourne, Parkville, Victoria 3052, Australia.,From the School of Science, Royal Melbourne Institute of Technology (RMIT) University, Bundoora, Victoria 3083, Australia.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts 02115.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab (F598) Heavy Chain
H
227N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab (F598) Light Chain
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 88.837α = 90.00
b = 104.067β = 90.00
c = 104.300γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Database references
  • Version 1.2: 2018-03-28
    Type: Data collection, Database references
  • Version 1.3: 2018-04-18
    Type: Data collection, Database references