8RDF

Crystal structure of Haemophilus influenzae type b (Hib) DP3 oligosaccharide bound to Fab CA4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope.

Nonne, F.Iacono, L.D.Bertuzzi, S.Unione, L.Proietti, D.Norais, N.Margarit, I.Adamo, R.Jimenez-Barbero, J.Carboni, F.Romano, M.R.

(2024) ACS Cent Sci 10: 978-987

  • DOI: https://doi.org/10.1021/acscentsci.3c01515
  • Primary Citation of Related Structures:  
    8RDA, 8RDF

  • PubMed Abstract: 

    Glycoconjugate vaccines so far licensed are generally composed of a native or size-reduced capsular polysaccharide conjugated to carrier proteins. Detailed information on the structural requirements necessary for CPS recognition is becoming the key to accelerating the development of next-generation improved glycoconjugate vaccines. Structural glycobiology studies using oligosaccharides (OS) complexed with functional monoclonal antibodies represent a powerful tool for gaining information on CPS immunological determinants at the atomic level. Herein, the minimal structural epitope of Haemophilus influenzae type b (Hib) CPS recognized by a functional human monoclonal antibody (hmAb) is reported. Short and well-defined Hib oligosaccharides originating from the depolymerization of the native CPS have been used to elucidate saccharide-mAb interactions by using a multidisciplinary approach combining surface plasmon resonance (SPR), saturation transfer difference-nanomagnetic resonance (STD-NMR), and X-ray crystallography. Our study demonstrates that the minimal structural epitope of Hib is comprised within two repeating units (RUs) where ribose and ribitol are directly engaged in the hmAb interaction, and the binding pocket fully accommodates two RUs without any additional involvement of a third one. Understanding saccharide antigen structural characteristics can provide the basis for the design of innovative glycoconjugate vaccines based on alternative technologies, such as synthetic or enzymatic approaches.


  • Organizational Affiliation

    GSK Vaccines Institute for Global Health, 53100 Siena, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab CA4 H chainA [auth H]224Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab CA4 L chainB [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H09 (Subject of Investigation/LOI)
Query on A1H09

Download Ideal Coordinates CCD File 
C [auth H]Haemophilus influenzae type b (Hib) DP3 oligosaccharide
C30 H59 O34 P3
MUJPLVAWHMKDRT-KFDLCVIWSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.928α = 90
b = 131.288β = 90
c = 144.964γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references