5UR8

Human antibody fragment (Fab) to meningococcal Factor H binding protein

• PDB DOI: https://doi.org/10.2210/pdb5UR8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-09 Released: 2018-02-14 
• Deposition Author(s): Beernink, P.T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.222 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 

Literature

Crystal structure reveals vaccine elicited bactericidal human antibody targeting a conserved epitope on meningococcal fHbp.

Lopez-Sagaseta, J., Beernink, P.T., Bianchi, F., Santini, L., Frigimelica, E., Lucas, A.H., Pizza, M., Bottomley, M.J.

(2018) Nat Commun 9: 528-528

• PubMed: 29410413 
• DOI: https://doi.org/10.1038/s41467-018-02827-7
• Primary Citation of Related Structures:  
  5O14, 5UR8


• PubMed Abstract: 
  

  Data obtained recently in the United Kingdom following a nationwide infant immunization program against serogroup B Neisseria meningitidis (MenB) reported >80% 4CMenB vaccine-mediated protection. Factor H-binding protein (fHbp) is a meningococcal virulence factor and a component of two new MenB vaccines. Here, we investigated the structural bases underlying the fHbp-dependent protective antibody response in humans, which might inform future antigen design efforts. We present the co-crystal structure of a human antibody Fab targeting fHbp. The vaccine-elicited Fab 1A12 is cross-reactive and targets an epitope highly conserved across the repertoire of three naturally occurring fHbp variants. The free Fab structure highlights conformational rearrangements occurring upon antigen binding. Importantly, 1A12 is bactericidal against MenB strains expressing fHbp from all three variants. Our results reveal important immunological features potentially contributing to the broad protection conferred by fHbp vaccination. Our studies fuel the rationale of presenting conserved protein epitopes when developing broadly protective vaccines.

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Organizational Affiliation: 

GSK Vaccines srl, Via Fiorentina 1, 53100, Siena, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.13 kDa 
• Atom Count: 3,809 
• Modelled Residue Count: 444 
• Deposited Residue Count: 452 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
human immunoglobulin gamma, heavy chain Fd fragment	A	235	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
human immunoglobulin gamma, kappa light chain	B	217	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.222 
• R-Value Work: 0.198 
• R-Value Observed: 0.199 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.9	α = 90
b = 131.9	β = 90
c = 90.381	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Beernink, P.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI099125

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description