3NSS

The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active sites

• PDB DOI: https://doi.org/10.2210/pdb3NSS/pdb

• Classification: HYDROLASE
• Organism(s): Influenza A virus (A/California/04/2009(H1N1))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-07-02 Released: 2010-09-22 
• Deposition Author(s): Li, Q., Qi, J.X., Zhang, W., Vavricka, C.J., Shi, Y., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site

Li, Q., Qi, J.X., Zhang, W., Vavricka, C.J., Shi, Y., Wei, J.H., Feng, E.G., Shen, J.S., Chen, J.L., Liu, D., He, J.H., Yan, J.H., Liu, H., Jiang, H.L., Teng, M.K., Li, X.B., Gao, G.F.

(2010) Nat Struct Mol Biol 17: 1266-1268

• PubMed: 20852645 
• DOI: https://doi.org/10.1038/nsmb.1909
• Primary Citation of Related Structures:  
  3NSS


• PubMed Abstract: 
  

  Influenza A virus neuraminidase can be classified into groups 1 and 2 on the basis of its primary structure. The main structural feature of group 1 neuraminidase is an extra cavity in the active site, the 150-cavity. Here we present the crystal structure of neuraminidase from the 2009 pandemic H1N1 influenza strain. In contrast to other characterized N1 neuraminidases, which are all members of group 1, 2009 H1N1 neuraminidase does not have a 150-cavity.

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Organizational Affiliation: 

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 87.3 kDa 
• Atom Count: 6,984 
• Modelled Residue Count: 774 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B	388	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for C3W5S3 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S3  Go to UniProtKB:  C3W5S3
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ACT	H [auth A], I [auth A], J [auth A], O [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	E [auth A], F [auth A], G [auth A], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.537	α = 90
b = 137.857	β = 90
c = 118.512	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Li, Q., Qi, J.X., Zhang, W., Vavricka, C.J., Shi, Y., Gao, G.F.

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary