8DOZ

Protective antibody against gonococcal lipooligosaccharide

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus
  • Expression System: Cricetulus griseus
  • Mutation(s): No 

  • Deposited: 2022-07-14 Released: 2023-06-21 
  • Deposition Author(s): Beernink, P.T.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Gonococcal Mimitope Vaccine Candidate Forms a Beta-Hairpin Turn and Binds Hydrophobically to a Therapeutic Monoclonal Antibody.

Beernink, P.T.Di Carluccio, C.Marchetti, R.Cerofolini, L.Carillo, S.Cangiano, A.Cowieson, N.Bones, J.Molinaro, A.Paduano, L.Fragai, M.Beernink, B.P.Gulati, S.Shaughnessy, J.Rice, P.A.Ram, S.Silipo, A.

(2024) JACS Au 4: 2617-2629

  • DOI: https://doi.org/10.1021/jacsau.4c00359
  • Primary Citation of Related Structures:  
    8DOZ, 8DUZ

  • PubMed Abstract: 

    The spread of multidrug-resistant strains of Neisseria gonorrhoeae , the etiologic agent of gonorrhea, represents a global health emergency. Therefore, the development of a safe and effective vaccine against gonorrhea is urgently needed. In previous studies, murine monoclonal antibody (mAb) 2C7 was raised against gonococcal lipooligosaccharide (LOS). mAb 2C7 elicits complement-dependent bactericidal activity against gonococci, and its glycan epitope is expressed by almost every clinical isolate. Furthermore, we identified a peptide, cyclic peptide 2 (CP2) that mimicked the 2C7 LOS epitope, elicited bactericidal antibodies in mice, and actively protected in a mouse vaginal colonization model. In this study, we performed structural analyses of mAb 2C7 and its complex with the CP2 peptide by X-ray crystallography, NMR spectroscopy, and molecular dynamics (MD) simulations. The crystal structure of Fab 2C7 bound to CP2 showed that the peptide adopted a beta-hairpin conformation and bound the Fab primarily through hydrophobic interactions. We employed NMR spectroscopy and MD simulations to map the 2C7 epitope and identify the bioactive conformation of CP2. We also used small-angle X-ray scattering (SAXS) and native mass spectrometry to obtain further information about the shape and assembly state of the complex. Collectively, our new structural information suggests strategies for humanizing mAb 2C7 as a therapeutic against gonococcal infection and for optimizing peptide CP2 as a vaccine antigen.


  • Organizational Affiliation

    Department of Pediatrics, University of California San Francisco, 5700 Martin Luther King Jr. Way, Oakland, California 94609, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 2C7, heavy chain Fd fragment
A, C
221Mus musculusMutation(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
Fab 2C7 lambda light chain
B, D
215Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40α = 92.13
b = 50.61β = 86.78
c = 106.21γ = 82.26
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI134868

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary
  • Version 1.3: 2024-11-27
    Changes: Database references