Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3BCD Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C 

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

Macromolecule Content

• Total Structure Weight: 108.57 kDa 
• Atom Count: 7465 
• Residue Count: 927 
• Unique protein chains: 4

3SDY

Crystal Structure of Broadly Neutralizing Antibody CR8020 Bound to the Influenza A H3 Hemagglutinin

• DOI: 10.2210/pdb3SDY/pdb

• Classification: Viral Protein/Immune System
• Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2)), Homo sapiens
• Expression System: Trichoplusia ni, Homo sapiens
• Mutation(s): No 


• Deposited: 2011-06-09 Released: 2011-07-20 
• Deposition Author(s): Ekiert, D.C., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Literature

A highly conserved neutralizing epitope on group 2 influenza A viruses.

Ekiert, D.C., Friesen, R.H., Bhabha, G., Kwaks, T., Jongeneelen, M., Yu, W., Ophorst, C., Cox, F., Korse, H.J., Brandenburg, B., Vogels, R., Brakenhoff, J.P., Kompier, R., Koldijk, M.H., Cornelissen, L.A., Poon, L.L., Peiris, M., Koudstaal, W., Wilson, I.A., Goudsmit, J.

(2011) Science 333: 843-850

• PubMed: 21737702 
• DOI: 10.1126/science.1204839
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Current flu vaccines provide only limited coverage against seasonal strains of influenza viruses. The identification of V(H)1-69 antibodies that broadly neutralize almost all influenza A group 1 viruses constituted a breakthrough in the influenza field. Here, we report the isolation and characterization of a human monoclonal antibody CR8020 with broad neutralizing activity against most group 2 viruses, including H3N2 and H7N7, which cause severe human infection. The crystal structure of Fab CR8020 with the 1968 pandemic H3 hemagglutinin (HA) reveals a highly conserved epitope in the HA stalk distinct from the epitope recognized by the V(H)1-69 group 1 antibodies. Thus, a cocktail of two antibodies may be sufficient to neutralize most influenza A subtypes and, hence, enable development of a universal flu vaccine and broad-spectrum antibody therapies.

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Organizational Affiliation: 

Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA1 chain	A	323	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Go to UniProtKB:  Q91MA7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Antibody CR8020, Heavy Chain	H	227	Homo sapiens	Mutation(s): 0  Gene Names: Immunoglobulin heavy chain locus (IGH)

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA2 chain	B	176	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0  Gene Names: HA
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Go to UniProtKB:  Q91MA7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Antibody CR8020, Light Chain	L	216	Homo sapiens	Mutation(s): 0  Gene Names: Immunoglobulin kappa chain locus (IGK)

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA	A, B	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
FUC	A, B	ALPHA-L-FUCOSE C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4	A, B, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	H	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.235 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 197.75	α = 90
b = 197.75	β = 90
c = 197.75	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
XPREP	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-09 
• Released Date: 2011-07-20 
Deposition Author(s): Ekiert, D.C., Wilson, I.A.

Revision History 

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Database references
• Version 2.0: 2019-12-25
  Changes: Data collection, Database references, Derived calculations, Polymer sequence