7DEA | pdb_00007dea

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck Northern China/22/2017 (H5N6)

• PDB DOI: https://doi.org/10.2210/pdb7DEA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2020-11-03 Released: 2021-11-03 
• Deposition Author(s): Sun, H., Sun, H., Song, J., Zhang, W., Wei, X., Qi, J., Gao, G.F., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Haemagglutinin and neuraminidase acid stability in H5N6 avian influenza virus confers infection adaptation in mammals

Sun, H., Sun, H., Song, J., Zhang, W., Qi, J., Gao, G.F., Liu, J.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 170.76 kDa 
• Atom Count: 11,980 
• Modeled Residue Count: 1,470 
• Deposited Residue Count: 1,470 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B [auth E], D [auth C]	319	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A7S7YCE5 (Influenza A virus) Explore A0A7S7YCE5  Go to UniProtKB:  A0A7S7YCE5
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	C [auth F], E [auth D], F [auth B]	171	Influenza A virus	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A6M2RI35 (Influenza A virus) Explore A0A6M2RI35  Go to UniProtKB:  A0A6M2RI35

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	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 (Subject of Investigation/LOI)	J [auth A], K [auth A], L [auth E], M [auth E], N [auth C], O [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: 2.84 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.413	α = 90
b = 109.367	β = 90.02
c = 135.913	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Sun, H., Sun, H., Song, J., Zhang, W., Wei, X., Qi, J., Gao, G.F., Liu, J.

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary