3S12

Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 1

• PDB DOI: https://doi.org/10.2210/pdb3S12/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/chicken/Hong Kong/YU562/2001(H5N1))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-05-14 Released: 2011-12-14 
• Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Heath, R.J., White, S.W., Russell, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

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: 59.56 kDa 
• Atom Count: 3,860 
• Modelled Residue Count: 476 
• Deposited Residue Count: 518 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A	336	Influenza A virus (A/chicken/Hong Kong/YU562/2001(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q80A30 (Influenza A virus (strain A/Chicken/Hong Kong/YU562/2001 H5N1 genotype B)) Explore Q80A30  Go to UniProtKB:  Q80A30

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B	182	Influenza A virus (A/chicken/Hong Kong/YU562/2001(H5N1))	Mutation(s): 0  Gene Names: HA
UniProt
Find proteins for Q80A30 (Influenza A virus (strain A/Chicken/Hong Kong/YU562/2001 H5N1 genotype B)) Explore Q80A30  Go to UniProtKB:  Q80A30

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.552	α = 90
b = 112.552	β = 90
c = 134.689	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Heath, R.J., White, S.W., Russell, C.J.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary