4N62

Crystal structure of hemagglutinin from an H7N9 influenza virus in complex with a sulfated receptor analog

• PDB DOI: https://doi.org/10.2210/pdb4N62/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/Shanghai/02/2013(H7N9))
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-10-11 Released: 2013-12-18 
• Deposition Author(s): Xu, R., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

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: 114.69 kDa 
• Atom Count: 7,839 
• Modelled Residue Count: 974 
• Deposited Residue Count: 1,008 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C	321	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21  Go to UniProtKB:  R4NN21

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2	B, D	183	Influenza A virus (A/Shanghai/02/2013(H7N9))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for R4NN21 (Influenza A virus) Explore R4NN21  Go to UniProtKB:  R4NN21

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose	F, G	3		N/A
Glycosylation Resources
GlyTouCan:  G99745QX GlyCosmos:  G99745QX GlyGen:  G99745QX

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.265 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.806	α = 90
b = 153.806	β = 90
c = 153.806	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Xu, R., Wilson, I.A.

Revision History  

• Version 1.0: 2013-12-18
  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