8BK2

X-ray structure of meningococcal factor H binding protein variant 2 in complex with a specific and bactericidal human monoclonal antibody 1B1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bactericidal human monoclonal antibody 1B1 shows specificity for meningococcal factor H binding protein variant 2 and displaces human factor H.

Veggi, D.Chesterman, C.C.Santini, L.Huang, Y.Pacchiani, N.Sierra, J.Chen, L.Laliberte, J.Bianchi, F.Cozzi, R.Frigimelica, E.Maione, D.Finco, O.Bottomley, M.J.

(2024) FASEB Bioadv 6: 235-248

  • DOI: https://doi.org/10.1096/fba.2023-00077
  • Primary Citation of Related Structures:  
    8BK2

  • PubMed Abstract: 

    Thousands of disease cases and hundreds of deaths occur globally each year due to invasive meningococcal disease. Neisseria meningitidis serogroup B (MenB) is the leading cause of such disease in developed countries. Two vaccines, 4CMenB and MenB-fHbp, that protect against MenB are available and include one or two forms respectively of factor H binding protein (fHbp), a key protective antigen. Studies of circulating meningococci have identified over 1380 different fHbp amino acid sequences, which form three immunologically distinct clusters, termed variants 1, 2, and 3. Neither of the current vaccines contains a variant 2 antigen, which is less well characterized than fHbp variants 1 and 3. We characterized the interaction of fHbp variant 2 with humAb 1B1 using biochemical methods and live meningococcal assays. Further, we determined the crystal structure of the complex at 2.4 Å resolution, clearly revealing the epitope and providing the first detailed report of an antibody with distinct specificity for fHbp variant 2. Extensive mutagenesis and binding studies elucidated key hotspots in the interface. This combination of structural and functional studies provides a molecular explanation for the bactericidal potency and specificity of humAb 1B1 for fHbp variant 2. Our studies, focused on fHbp variant 2, expand the understanding of this previously under characterized group of the vast family of variants of fHbp, a virulence factor present on all meningococci. Moreover, the definition of a protective conformational epitope on fHbp variant 2 may support the design and development of novel variant 2-containing MenB vaccines affording greater breadth of protection.


  • Organizational Affiliation

    GSK Siena Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Factor H-binding protein
A, B, C
260Neisseria meningitidis serogroup BMutation(s): 0 
Gene Names: fhbp
UniProt
Find proteins for C6JW56 (Neisseria meningitidis)
Explore C6JW56 
Go to UniProtKB:  C6JW56
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6JW56
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy chainD [auth H],
F [auth D],
H [auth F]
226Homo 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
Fab light ChainsE [auth L],
G [auth E],
I [auth G]
216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
N [auth L]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
T [auth G]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
O [auth L](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IMD
Query on IMD

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L [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]
K [auth B]
P [auth D]
Q [auth D]
R [auth E]
J [auth A],
K [auth B],
P [auth D],
Q [auth D],
R [auth E],
S [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.153α = 90
b = 135.641β = 105.18
c = 121.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Database references