Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 173.90 kDa 
• Atom Count: 12892 
• Modelled Residue Count: 1490 
• Deposited Residue Count: 1524 
• Unique protein chains: 2

4M4Y

Crystal structure of a 2009 H1N1 influenza virus hemagglutinin with a stabilization mutation HA2 E47G

• PDB DOI: 10.2210/pdb4M4Y/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus (A/California/04/2009(H1N1))
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2013-08-07 Released: 2013-09-25 
• Deposition Author(s): Zhu, X., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Literature

Antibody Recognition of the Pandemic H1N1 Influenza Virus Hemagglutinin Receptor Binding Site.

Hong, M., Lee, P.S., Hoffman, R.M., Zhu, X., Krause, J.C., Laursen, N.S., Yoon, S.I., Song, L., Tussey, L., Crowe, J.E., Ward, A.B., Wilson, I.A.

(2013) J Virol 87: 12471-12480

• PubMed: 24027321 
• DOI: 10.1128/JVI.01388-13
• Primary Citation of Related Structures:  
  4M4Y, 4M5Y, 4M5Z


• PubMed Abstract: 
  

Influenza virus is a global health concern due to its unpredictable pandemic potential. This potential threat was realized in 2009 when an H1N1 virus emerged that resembled the 1918 virus in antigenicity but fortunately was not nearly as deadly. 5J8 is a human antibody that potently neutralizes a broad spectrum of H1N1 viruses, including the 1918 and 2009 pandemic viruses. Here, we present the crystal structure of 5J8 Fab in complex with a bacterially expressed and refolded globular head domain from the hemagglutinin (HA) of the A/California/07/2009 (H1N1) pandemic virus. 5J8 recognizes a conserved epitope in and around the receptor binding site (RBS), and its HCDR3 closely mimics interactions of the sialic acid receptor. Electron microscopy (EM) reconstructions of 5J8 Fab in complex with an HA trimer from a 1986 H1 strain and with an engineered stabilized HA trimer from the 2009 H1 pandemic virus showed a similar mode of binding. As for other characterized RBS-targeted antibodies, 5J8 uses avidity to extend its breadth and affinity against divergent H1 strains. 5J8 selectively interacts with HA insertion residue 133a, which is conserved in pandemic H1 strains and has precluded binding of other RBS-targeted antibodies. Thus, the RBS of divergent HAs is targeted by 5J8 and adds to the growing arsenal of common recognition motifs for design of therapeutics and vaccines. Moreover, consistent with previous studies, the bacterially expressed H1 HA properly refolds, retaining its antigenic structure, and presents a low-cost and rapid alternative for engineering and manufacturing candidate flu vaccines.

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Organizational Affiliation: 

Department of Integrative Structural and Computational Biology.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 subunit	A, B [auth C], C [auth E]	331	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 0  Gene Names: HA, hemagglutinin
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1  Go to UniProtKB:  C3W5S1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 subunit	D [auth B], E [auth D], F	177	Influenza A virus (A/California/04/2009(H1N1))	Mutation(s): 1  Gene Names: HA, hemagglutinin
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1)) Explore C3W5S1  Go to UniProtKB:  C3W5S1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46874CY GlyCosmos:  G46874CY GlyGen:  G46874CY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth A], L [auth C], M [auth C], N [auth C], O [auth E], P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.232 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.367	α = 90
b = 132.174	β = 90
c = 201.809	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-07 
• Released Date: 2013-09-25 
Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-11-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary