Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 12-mer -A6B3C3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 318484.50 
• Atom Count: 21672 
• Residue Count: 2847 
• Unique protein chains: 4

4NM8

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

• DOI: 10.2210/pdb4NM8/pdb

• Classification: viral protein/immune system
• Organism(s): Influenza A virus (strain A/Hong Kong/1/1968 H3N2), Homo sapiens
• Expression System: Trichoplusia ni


• Deposited: 2013-11-14 Released: 2013-12-25 
• Deposition Author(s): Lee, P.S., Wilson, I.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.0041 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 

Literature

A common solution to group 2 influenza virus neutralization.

Friesen, R.H., Lee, P.S., Stoop, E.J., Hoffman, R.M., Ekiert, D.C., Bhabha, G., Yu, W., Juraszek, J., Koudstaal, W., Jongeneelen, M., Korse, H.J., Ophorst, C., Brinkman-van der Linden, E.C., Throsby, M., Kwakkenbos, M.J., Bakker, A.Q., Beaumont, T., Spits, H., Kwaks, T., Vogels, R., Ward, A.B., Goudsmit, J., Wilson, I.A.

(2014) Proc.Natl.Acad.Sci.USA 111: 445-450

• PubMed: 24335589 
• DOI: 10.1073/pnas.1319058110
• Primary Citation of Related Structures:  
  4NM4


• PubMed Abstract: 
  

The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one human bnAb (CR8020) specifically recognizing group 2 influenza A viruses has been previously characterized that binds to a highly conserved epitope at the base of the hemagglutinin (HA) stem and has neutralizing activity against H3, H7, and H10 viruses. Here, we report a second group 2 bnAb, CR8043, which was derived from a different germ-line gene encoding a highly divergent amino acid sequence. CR8043 has in vitro neutralizing activity against H3 and H10 viruses and protects mice against challenge with a lethal dose of H3N2 and H7N7 viruses. The crystal structure and EM reconstructions of the CR8043-H3 HA complex revealed that CR8043 binds to a site similar to the CR8020 epitope but uses an alternative angle of approach and a distinct set of interactions. The identification of another antibody against the group 2 stem epitope suggests that this conserved site of vulnerability has great potential for design of therapeutics and vaccines.

---

Organizational Affiliation: 

Crucell Vaccine Institute, Janssen Center of Excellence for Immunoprophylaxis, 2333 CN, Leiden, The Netherlands.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA1 Chain	A, C, E	323	Influenza A virus (strain 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: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemagglutinin HA2 Chain	B, D, F	176	Influenza A virus (strain 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 CR8043, Light Chain	L, M, N	220	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
Find proteins for P01834 (Homo sapiens) Go to UniProtKB:  P01834

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Antibody CR8043, Heavy Chain	H, I, J	230	Homo sapiens	Mutation(s): 0
Find proteins for S6C4S0 (Homo sapiens) Go to UniProtKB:  S6C4S0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B, C, D, E, F	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.0041 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 241.491	α = 90.00
b = 142.355	β = 133.46
c = 170.725	γ = 90.00

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-14 
• Released Date: 2013-12-25 
• Deposition Author(s): Lee, P.S., Wilson, I.A.

Revision History 

• Version 1.0: 2013-12-25
  Type: Initial release
• Version 1.1: 2014-01-22
  Type: Database references
• Version 1.2: 2017-06-21
  Type: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2017-12-06
  Type: Database references