Biological Assembly 1  

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

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: 318.38 kDa 
• Atom Count: 21672 
• Modelled Residue Count: 2757 
• Deposited Residue Count: 2847 
• Unique protein chains: 4

4NM8

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

• PDB DOI: 10.2210/pdb4NM8/pdb

• Classification: viral protein/immune system
• Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2)), Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

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 U S A 111: 445-450

• PubMed: 24335589 
• DOI: 10.1073/pnas.1319058110
• Primary Citation of Related Structures:  
  4NM4, 4NM8


• 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.

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Organizational Affiliation: 

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

Macromolecules

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

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody CR8043, Light Chain	G [auth L], I [auth M], K [auth N]	220	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody CR8043, Heavy Chain	H, J [auth I], L [auth J]	230	Homo sapiens	Mutation(s): 0  Gene Names: DKFZp686I15212, DKFZp686P15220
UniProt
Find proteins for S6C4S0 (Homo sapiens) Explore S6C4S0  Go to UniProtKB:  S6C4S0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], N [auth K], O, P, Q, R	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	S [auth B], T [auth C], U [auth C], V [auth D], W [auth E], X [auth E], Y [auth E], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.292 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 241.491	α = 90
b = 142.355	β = 133.46
c = 170.725	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2017-12-06
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary