8G3Z | pdb_00008g3z

Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in complex with 4 FNI17 Fab molecules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8G3Z

This is version 1.3 of the entry. See complete history

Literature

A pan-influenza antibody inhibiting neuraminidase via receptor mimicry.

Momont, C.Dang, H.V.Zatta, F.Hauser, K.Wang, C.di Iulio, J.Minola, A.Czudnochowski, N.De Marco, A.Branch, K.Donermeyer, D.Vyas, S.Chen, A.Ferri, E.Guarino, B.Powell, A.E.Spreafico, R.Yim, S.S.Balce, D.R.Bartha, I.Meury, M.Croll, T.I.Belnap, D.M.Schmid, M.A.Schaiff, W.T.Miller, J.L.Cameroni, E.Telenti, A.Virgin, H.W.Rosen, L.E.Purcell, L.A.Lanzavecchia, A.Snell, G.Corti, D.Pizzuto, M.S.

(2023) Nature 618: 590-597

  • DOI: https://doi.org/10.1038/s41586-023-06136-y
  • Primary Citation Related Structures: 
    8G30, 8G3M, 8G3N, 8G3O, 8G3P, 8G3Q, 8G3R, 8G3V, 8G3Z, 8G40

  • PubMed Abstract: 

    Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift 1 and suboptimal immune responses 2 . Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.


  • Organizational Affiliation
    • Vir Biotechnology, San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 414.79 kDa 
  • Atom Count: 19,485 
  • Modeled Residue Count: 2,512 
  • Deposited Residue Count: 3,768 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FNI17 Fab heavy chainA [auth H],
C [auth E],
E [auth G],
G [auth J]
231Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FNI17 Fab light chainB [auth L],
D [auth F],
F [auth I],
H [auth K]
215Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NeuraminidaseI [auth A],
J [auth B],
K [auth C],
L [auth D]
496Influenza B virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for R4KV67 (Influenza B virus)
Explore R4KV67 
Go to UniProtKB:  R4KV67
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4KV67
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
N [auth A]
O [auth A]
R [auth B]
S [auth B]
U [auth C]
N [auth A],
O [auth A],
R [auth B],
S [auth B],
U [auth C],
V [auth C],
X [auth D],
Y [auth D]
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
M [auth A],
P [auth A],
Q [auth B],
T [auth C],
W [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-06-28
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Data collection, Structure summary