3ZTJ

Structure of influenza A neutralizing antibody selected from cultures of single human plasma cells in complex with human H3 Influenza haemagglutinin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 
    0.284 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation   3D Report Full Report


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

This is version 2.1 of the entry. See complete history


Literature

A Neutralizing Antibody Selected from Plasma Cells that Binds to Group 1 and Group 2 Influenza a Hemagglutinins.

Corti, D.Voss, J.E.Gamblin, S.J.Codoni, G.Macagno, A.Jarrossay, D.Vachieri, S.G.Pinna, D.Minola, A.Vanzetta, F.Silacci, C.Fernandez-Rodriguez, B.M.Agatic, G.Bianchi, S.Giacchetto-Sasselli, I.Calder, L.Sallusto, F.Collins, P.J.Haire, L.F.Temperton, N.Langedijk, J.P.M.Skehel, J.J.Lanzavecchia, A.

(2011) Science 333: 850

  • DOI: https://doi.org/10.1126/science.1205669
  • Primary Citation of Related Structures:  
    3ZTJ, 3ZTN

  • PubMed Abstract: 

    The isolation of broadly neutralizing antibodies against influenza A viruses has been a long-sought goal for therapeutic approaches and vaccine design. Using a single-cell culture method for screening large numbers of human plasma cells, we isolated a neutralizing monoclonal antibody that recognized the hemagglutinin (HA) glycoprotein of all 16 subtypes and neutralized both group 1 and group 2 influenza A viruses. Passive transfer of this antibody conferred protection to mice and ferrets. Complexes with HAs from the group 1 H1 and the group 2 H3 subtypes analyzed by x-ray crystallography showed that the antibody bound to a conserved epitope in the F subdomain. This antibody may be used for passive protection and to inform vaccine design because of its broad specificity and neutralization potency.


  • Organizational Affiliation

    Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ HA1 CHAIN
A, C, E
329Influenza A virus (A/Aichi/2/1968(H3N2))Mutation(s): 0 
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ HA2 CHAIN
B, D, F
175Influenza A virus (A/Aichi/2/1968(H3N2))Mutation(s): 0 
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2))
Explore Q91MA7 
Go to UniProtKB:  Q91MA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91MA7
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
FI6V3 ANTIBODY HEAVY CHAIN
G, I, K
226Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
FI6V3 ANTIBODY LIGHT CHAIN
H, J, L
218Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, O, T, X
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N, P, Q, R, S
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free:  0.284 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.488α = 90
b = 193.428β = 90
c = 213.748γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



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: 2011-08-10
    Type: Initial release
  • Version 1.1: 2011-08-24
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2012-09-05
    Changes: Derived calculations
  • Version 1.3: 2013-05-29
    Changes: Other
  • Version 1.4: 2017-01-25
    Changes: Atomic model, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary