7DEB | pdb_00007deb

Structure of an avian influenza H5 hemagglutinin from the influenza virus A/duck/Eastern China/L0230/2010 (H5N2)

• PDB DOI: https://doi.org/10.2210/pdb7DEB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/duck/Eastern China/L0321/2010(H5N2))
• 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., Qi, J., Gao, G.F., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (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: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.95 kDa 
• Atom Count: 12,488 
• Modeled Residue Count: 1,482 
• Deposited Residue Count: 1,515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	505	Influenza A virus (A/duck/Eastern China/L0321/2010(H5N2))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for A0A0X7YU24 (Influenza A virus) Explore A0A0X7YU24  Go to UniProtKB:  A0A0X7YU24
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
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	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	E, F	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	G [auth A], H [auth B], I [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: 2.60 Å
• R-Value Free:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.956	α = 90
b = 164.864	β = 90
c = 230.201	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Sun, H., Sun, H., Song, J., Zhang, W., 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: 2024-11-20
  Changes: Structure summary