6N08 | pdb_00006n08

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

• PDB DOI: https://doi.org/10.2210/pdb6N08/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Netherlands/209/1980(H3N2))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-11-06 Released: 2019-05-15 
• Deposition Author(s): Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

Dai, Y.N., Fremont, D.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.03 kDa 
• Atom Count: 13,045 
• Modeled Residue Count: 1,464 
• Deposited Residue Count: 1,491 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	497	Influenza A virus (A/Netherlands/209/1980(H3N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for H9XIV6 (Influenza A virus) Explore H9XIV6  Go to UniProtKB:  H9XIV6
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, G, H, J, K, M	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, I, L, N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	O [auth A], P [auth A], Q [auth A], R [auth B], S [auth C], T [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.99	α = 90
b = 188.77	β = 109.82
c = 108.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• 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, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary