4JUL | pdb_00004jul

Crystal structure of H5N1 influenza virus hemagglutinin, clade 2.3.4

• PDB DOI: https://doi.org/10.2210/pdb4JUL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/duck/Laos/3295/2006(H5N1))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-03-25 Released: 2014-05-07 
• Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

To be published

DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 350.56 kDa 
• Atom Count: 23,752 
• Modeled Residue Count: 2,950 
• Deposited Residue Count: 3,066 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E, G [auth H], I [auth J], K [auth L]	329	Influenza A virus (A/duck/Laos/3295/2006(H5N1))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q00G25 (Influenza A virus) Explore Q00G25  Go to UniProtKB:  Q00G25
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D, F, H [auth I], J [auth K], L [auth M]	182	Influenza A virus (A/duck/Laos/3295/2006(H5N1))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q00G25 (Influenza A virus) Explore Q00G25  Go to UniProtKB:  Q00G25

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	M [auth G], N, O, P	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	Q [auth A], R [auth C], S [auth C], T [auth E], U [auth H], V [auth J], W [auth J], X [auth L]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.584	α = 83.94
b = 71.557	β = 85.46
c = 247.054	γ = 60.68

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.J.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary