5NQP | pdb_00005nqp

Structure of a fHbp(V1.4):PorA(P1.16) chimera. Fusion at fHbp position 151.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 
    0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NQP

This is version 1.3 of the entry. See complete history

Literature

Structure-based design of chimeric antigens for multivalent protein vaccines.

Hollingshead, S.Jongerius, I.Exley, R.M.Johnson, S.Lea, S.M.Tang, C.M.

(2018) Nat Commun 9: 1051-1051

  • DOI: https://doi.org/10.1038/s41467-018-03146-7
  • Primary Citation Related Structures: 
    5NQP, 5NQX, 5NQY, 5NQZ

  • PubMed Abstract: 

    There is an urgent need to develop vaccines against pathogenic bacteria. However, this is often hindered by antigenic diversity and difficulties encountered manufacturing membrane proteins. Here we show how to use structure-based design to develop chimeric antigens (ChAs) for subunit vaccines. ChAs are generated against serogroup B Neisseria meningitidis (MenB), the predominant cause of meningococcal disease in wealthy countries. MenB ChAs exploit factor H binding protein (fHbp) as a molecular scaffold to display the immunogenic VR2 epitope from the integral membrane protein PorA. Structural analyses demonstrate fHbp is correctly folded and the PorA VR2 epitope adopts an immunogenic conformation. In mice, immunisation with ChAs generates fHbp and PorA antibodies that recognise the antigens expressed by clinical MenB isolates; these antibody responses correlate with protection against meningococcal disease. Application of ChAs is therefore a potentially powerful approach to develop multivalent subunit vaccines, which can be tailored to circumvent pathogen diversity.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.

Macromolecule Content 

  • Total Structure Weight: 89.41 kDa 
  • Atom Count: 6,007 
  • Modeled Residue Count: 776 
  • Deposited Residue Count: 813 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Factor H binding protein variant B16_001,Major outer membrane protein P.IA,Factor H binding protein variant B16_001A [auth C],
B [auth A],
C [auth B]
271Neisseria meningitidisNeisseria meningitidis serogroup CMutation(s): 0 
Gene Names: fhbpporA
UniProt
Find proteins for P13415 (Neisseria meningitidis serogroup C)
Explore P13415 
Go to UniProtKB:  P13415
Find proteins for Q6VS06 (Neisseria meningitidis)
Explore Q6VS06 
Go to UniProtKB:  Q6VS06
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP13415Q6VS06
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth C],
M [auth A],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth C]
F [auth C]
G [auth C]
H [auth C]
I [auth C]
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
N [auth A],
O [auth A],
S [auth B],
T [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth C],
L [auth C],
P [auth A],
Q [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free:  0.239 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.72α = 90
b = 171.42β = 90
c = 131.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG0900888

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary