6QNA | pdb_00006qna

Structure of bovine anti-RSV hybrid Fab B13HC-B4LC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6QNA

This is version 1.3 of the entry. See complete history

Literature

The role of the light chain in the structure and binding activity of two cattle antibodies that neutralize bovine respiratory syncytial virus.

Ren, J.Nettleship, J.E.Harris, G.Mwangi, W.Rhaman, N.Grant, C.Kotecha, A.Fry, E.Charleston, B.Stuart, D.I.Hammond, J.Owens, R.J.

(2019) Mol Immunol 112: 123-130

  • DOI: https://doi.org/10.1016/j.molimm.2019.04.026
  • Primary Citation Related Structures: 
    6QN7, 6QN8, 6QN9, 6QNA

  • PubMed Abstract: 

    Cattle antibodies have unusually long CDR3 loops in their heavy chains (HCs), and limited light chain (LC) diversity, raising the question of whether these mask the effect of LC variation on antigen recognition. We have investigated the role of the LC in the structure and activity of two neutralizing cattle antibodies (B4 and B13) that bind the F protein of bovine respiratory syncytial virus (bRSV). Recombinant Fab fragments of B4 and B13 bound bRSV infected cells and showed similar affinities for purified bRSV F protein. Exchanging the LCs between the Fab fragments produced hybrid Fabs: B13* (B13 HC/B4 LC) and B4* (B4 HC/B13 LC). The affinity of B13* to the F protein was found to be two-fold lower than B13 whilst the binding affinity of B4* was reduced at least a hundred-fold compared to B4 such that it no longer bound to bRSV infected cells. Comparison of the structures of B4 and B13 with their LC exchanged counterparts B4* and B13* showed that paratope of the HC variable domain (VH) of B4 was disrupted on pairing with the B13 LC, consistent with the loss of binding activity. By contrast, B13 H3 adopts a similar conformation when paired with either B13 or B4 LCs. These observations confirm the expected key role of the extended H3 loop in antigen-binding by cattle antibodies but also show that the quaternary LC/HC subunit interaction can be crucial for its presentation and thus the LC variable domain (VL) is also important for antigen recognition.


  • Organizational Affiliation
    • The Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford, OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 194.15 kDa 
  • Atom Count: 13,139 
  • Modeled Residue Count: 1,760 
  • Deposited Residue Count: 1,828 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
B13 Heavy chainA [auth H],
C [auth A],
E [auth C],
G [auth E]
243Bos taurusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
B4 light chainB [auth L],
D [auth B],
F [auth D],
H [auth F]
214Bos taurusMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.44α = 89.66
b = 76.27β = 87.35
c = 130.03γ = 88.6
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
Wellcome TrustUnited Kingdom101122/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary