5N4G | pdb_00005n4g

human Fab fragment 12E1 against NHBA from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.268 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structures of human Fabs targeting the Bexsero meningococcal vaccine antigen NHBA.

Maritan, M.Cozzi, R.Lo Surdo, P.Veggi, D.Bottomley, M.J.Malito, E.

(2017) Acta Crystallogr F Struct Biol Commun 73: 305-314

  • DOI: https://doi.org/10.1107/S2053230X17006021
  • Primary Citation Related Structures: 
    5N4G, 5N4J

  • PubMed Abstract: 

    Neisserial heparin-binding antigen (NHBA) is a surface-exposed lipoprotein from Neisseria meningitidis and is a component of the meningococcus B vaccine Bexsero. As part of a study to characterize the three-dimensional structure of NHBA and the molecular basis of the human immune response to Bexsero, the crystal structures of two fragment antigen-binding domains (Fabs) isolated from human monoclonal antibodies targeting NHBA were determined. Through a high-resolution analysis of the organization and the amino-acid composition of the CDRs, these structures provide broad insights into the NHBA epitopes recognized by the human immune system. As expected, these Fabs also show remarkable structural conservation, as shown by a structural comparison of 15 structures of apo Fab 10C3 which were obtained from crystals grown in different crystallization conditions and were solved while searching for a complex with a bound NHBA fragment or epitope peptide. This study also provides indirect evidence for the intrinsically disordered nature of two N-terminal regions of NHBA.


  • Organizational Affiliation
    • GSK Vaccines, Via Fiorentina 1, 53100 Siena, Italy.

Macromolecule Content 

  • Total Structure Weight: 52.45 kDa 
  • Atom Count: 3,434 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 476 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEAVY CHAINA [auth H]257Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LIGHT CHAINB [auth L]219Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.268 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.88α = 90
b = 82.16β = 90
c = 100.39γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary