9GQT | pdb_00009gqt

influenza neuraminidase hybrid N1/09


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-guided loop grafting improves expression and stability of influenza neuraminidase for vaccine development.

Rijal, P.Wei, L.Paesen, G.C.Stuart, D.I.Haworth, M.Huang, K.A.Bowden, T.A.Townsend, A.R.M.

(2025) Elife 14

  • DOI: https://doi.org/10.7554/eLife.105317
  • Primary Citation of Related Structures:  
    9GQQ, 9GQT, 9GQX

  • PubMed Abstract: 

    Influenza virus neuraminidase (NA) is a crucial target for protective antibodies, yet the development of recombinant NA protein as a vaccine has been held back by instability and variable expression. We have taken a pragmatic approach to improving expression and stability of NA by grafting antigenic surface loops from low-expressing NA proteins onto the scaffold of high-expressing counterparts. The resulting hybrid proteins retained the antigenic properties of the loop donor while benefiting from the high-yield expression, stability, and tetrameric structure of the loop recipient. These hybrid proteins were recognised by a broad set of human monoclonal antibodies elicited by influenza infection or vaccination, with X-ray structures validating the accurate structural conformation of the grafted loops and the enzymatic cavity. Immunisation of mice with NA hybrids induced inhibitory antibodies to the loop donor and protected against lethal influenza challenge. This pragmatic technique offers a robust solution for improving the expression and stability of influenza NA proteins for vaccine development.


  • Organizational Affiliation
    • Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase
A, B
511unidentified influenza virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for A0A509GK44 (Influenza A virus)
Explore A0A509GK44 
Go to UniProtKB:  A0A509GK44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A509GK44
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.089α = 90
b = 92.089β = 90
c = 146.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/S007555/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Database references