6V46 | pdb_00006v46

The crystal structure of hemagglutinin from A/turkey/Ontario/6118/1968 (H8N4)

• PDB DOI: https://doi.org/10.2210/pdb6V46/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-11-27 Released: 2020-06-17 
• Deposition Author(s): Yang, H., Stevens, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins

Yang, H., Carney, P.J., Chang, J., Stevens, J.

(2020) Heliyon 6: e04068

• DOI: https://doi.org/10.1016/j.heliyon.2020.e04068

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 177.84 kDa 
• Atom Count: 12,485 
• Modeled Residue Count: 1,467 
• Deposited Residue Count: 1,542 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	331	Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P03456 (Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)) Explore P03456  Go to UniProtKB:  P03456
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	183	Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for P03456 (Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)) Explore P03456  Go to UniProtKB:  P03456

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J, L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.047	α = 90
b = 98.086	β = 115.2
c = 132.735	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Currently 6V46 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Yang, H., Stevens, J.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, 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: 2024-10-16
  Changes: Structure summary