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 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 Chain
A, C, E
323Influenza 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 Groups  
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UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 Chain
B, D, F
176Influenza 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 Groups  
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UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence 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)
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Go to UniProtKB:  P01834
PHAROS:  P01834
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UniProt GroupP01834
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence 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
MoleculeChains Length2D Diagram Glycosylation3D 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,
2N-Glycosylation
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 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

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
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-27
    Changes: Structure summary