Biological Assembly 1  

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Hetero 24-mer - A8B8C8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 181.92 kDa 
• Atom Count: 12,932 
• Modelled Residue Count: 1,643 
• Deposited Residue Count: 1,644 
• Unique protein chains: 3

 4QNP

Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody

• PDB DOI:  https://doi.org/10.2210/pdb4QNP/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Influenza A virus, Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2014-06-18 Released: 2015-02-11 
• Deposition Author(s): Wan, H.Q., Yang, H., Shore, D.A., Garten, R.J., Couzens, L., Gao, J., Jiang, L.L., Carney, P.J., Villanueva, J., Stevens, J., Eichelberger, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Structural characterization of a protective epitope spanning A(H1N1)pdm09 influenza virus neuraminidase monomers.

Wan, H., Yang, H., Shore, D.A., Garten, R.J., Couzens, L., Gao, J., Jiang, L., Carney, P.J., Villanueva, J., Stevens, J., Eichelberger, M.C.

(2015) Nat Commun 6: 6114-6114

• PubMed: 25668439 
• DOI: https://doi.org/10.1038/ncomms7114
• Primary Citation of Related Structures:  
  4QNP


• PubMed Abstract: 
  

A(H1N1)pdm09 influenza A viruses predominated in the 2013-2014 USA influenza season, and although most of these viruses remain sensitive to Food and Drug Administration-approved neuraminidase (NA) inhibitors, alternative therapies are needed. Here we show that monoclonal antibody CD6, selected for binding to the NA of the prototypic A(H1N1)pdm09 virus, A/California/07/2009, protects mice against lethal virus challenge. The crystal structure of NA in complex with CD6 Fab reveals a unique epitope, where the heavy-chain complementarity determining regions (HCDRs) 1 and 2 bind one NA monomer, the light-chain CDR2 binds the neighbouring monomer, whereas HCDR3 interacts with both monomers. This 30-amino-acid epitope spans the lateral face of an NA dimer and is conserved among circulating A(H1N1)pdm09 viruses. These results suggest that the large, lateral CD6 epitope may be an effective target of antibodies selected for development as therapeutic agents against circulating H1N1 influenza viruses.

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Organizational Affiliation: 

Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland 20993, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B	386	Influenza A virus	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for D5KL82 (Influenza A virus) Explore D5KL82  Go to UniProtKB:  D5KL82

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
neutralizing antibody, light chain	C [auth F], E [auth L]	212	Mus musculus	Mutation(s): 0  Gene Names: Igkc
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
neutralizing antibody, heavy chain	D [auth E], F [auth H]	224	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C], H [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	K [auth A], L [auth A], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.29	α = 90
b = 202.951	β = 90
c = 143.968	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Wan, H.Q., Yang, H., Shore, D.A., Garten, R.J., Couzens, L., Gao, J., Jiang, L.L., Carney, P.J., Villanueva, J., Stevens, J., Eichelberger, M.C.

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary