6MCX

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) RECOMBINANT HEAD DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb6MCX/pdb

• Classification: hydrolase, viral protein
• Organism(s): Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2018-09-02 Released: 2019-01-23 
• Deposition Author(s): Streltsov, V.A., Schmidt, P., McKimm-Breschkin, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.147 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk.

Streltsov, V.A., Schmidt, P.M., McKimm-Breschkin, J.L.

(2019) Acta Crystallogr F Struct Biol Commun 75: 89-97

• PubMed: 30713159 
• DOI: https://doi.org/10.1107/S2053230X18017892
• Primary Citation of Related Structures:  
  6CRD, 6D3B, 6MCX


• PubMed Abstract: 
  

  The influenza neuraminidase (NA) is a homotetramer with head, stalk, transmembrane and cytoplasmic regions. The structure of the NA head with a stalk has never been determined. The NA head from an N9 subtype influenza A virus, A/tern/Australia/G70C/1975 (H1N9), was expressed with an artificial stalk derived from the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The NA was successfully crystallized both with and without the TB stalk, and the structures were determined to 2.6 and 2.3 Å resolution, respectively. Comparisons of the two NAs with the native N9 NA structure from egg-grown virus showed that the artificial TB stalk maintained the native NA head structure, supporting previous biological observations.

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Organizational Affiliation: 

CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia.

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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 45.72 kDa 
• Atom Count: 3,590 
• Modelled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	388	Influenza A virus (A/tern/Australia/G70C/1975(H11N9))	Mutation(s): 0  EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)) Explore P03472  Go to UniProtKB:  P03472
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH GlyCosmos:  G46836GH GlyGen:  G46836GH

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.206 
• R-Value Work: 0.147 
• R-Value Observed: 0.151 
• Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.721	α = 90
b = 180.721	β = 90
c = 180.721	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Streltsov, V.A., Schmidt, P., McKimm-Breschkin, J.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-11-13
  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: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary