4NM8

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


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 

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This is version 2.0 of the entry. See complete history


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

  • 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 ChainA, C, E323Influenza 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))
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Go to UniProtKB:  Q91MA7
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UniProt GroupQ91MA7
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2 ChainB, D, F176Influenza 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))
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Go to UniProtKB:  Q91MA7
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UniProt GroupQ91MA7
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody CR8043, Light ChainG [auth L],
I [auth M],
K [auth N]
220Homo sapiensMutation(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
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UniProt GroupP01834
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody CR8043, Heavy ChainH,
J [auth I],
L [auth J]
230Homo sapiensMutation(s): 0 
Gene Names: DKFZp686I15212DKFZp686P15220
UniProt
Find proteins for S6C4S0 (Homo sapiens)
Explore S6C4S0 
Go to UniProtKB:  S6C4S0
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UniProt GroupS6C4S0
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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,
M [auth G],
N [auth K],
O,
P,
Q,
R
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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 = 241.491α = 90
b = 142.355β = 133.46
c = 170.725γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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