4O5I

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus.

Lee, P.S.Ohshima, N.Stanfield, R.L.Yu, W.Iba, Y.Okuno, Y.Kurosawa, Y.Wilson, I.A.

(2014) Nat Commun 5: 3614-3614

  • DOI: 10.1038/ncomms4614
  • Primary Citation of Related Structures:  
    4O58, 4O5I, 4O5L, 4O5N

  • PubMed Abstract: 
  • Influenza viruses present a significant health challenge each year, as in the H3N2 epidemic of 2012-2013. Here we describe an antibody, F045-092, that possesses broadly neutralizing activity against the entire H3 subtype and accommodates the natural variation and additional glycosylation in all strains tested from 1963 to 2011 ...

    Influenza viruses present a significant health challenge each year, as in the H3N2 epidemic of 2012-2013. Here we describe an antibody, F045-092, that possesses broadly neutralizing activity against the entire H3 subtype and accommodates the natural variation and additional glycosylation in all strains tested from 1963 to 2011. Crystal structures of F045-092 in complex with HAs from 1975 and 2011 H3N2 viruses reveal the structural basis for its neutralization breadth through insertion of its 23-residue HCDR3 into the receptor-binding site that involves striking receptor mimicry. F045-092 extends its recognition to divergent subtypes, including H1, H2 and H13, using the enhanced avidity of its IgG to overcome lower-affinity Fab binding, as observed with other antibodies that target the receptor-binding site. This unprecedented level of antibody cross-reactivity against the H3 subtype can potentially inform on development of a pan-H3 vaccine or small-molecule therapeutics.


    Organizational Affiliation

    1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2] The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E, G, I, K
A, C, E, G, I, K
323Influenza A virus (A/Singapore/H2011.447/2011(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for R9U684 (Influenza A virus)
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Go to UniProtKB:  R9U684
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR9U684
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F, H, J, L
B, D, F, H, J, L
176Influenza A virus (A/Singapore/H2011.447/2011(H3N2))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for R9U684 (Influenza A virus)
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Go to UniProtKB:  R9U684
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UniProt GroupR9U684
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab F045-092 heavy chain
M, O, Q, S, U, W
M, O, Q, S, U, W
240Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6C4S0 (Homo sapiens)
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UniProt GroupS6C4S0
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab F045-092 light chain
N, P, R, T, V, X
N, P, R, T, V, X
216Homo sapiensMutation(s): 0 
Gene Names: IGL@IGLC2
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Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AB [auth 0],
DB [auth 3],
FB [auth 5],
GB [auth 6],
IA [auth i],
AB [auth 0],
DB [auth 3],
FB [auth 5],
GB [auth 6],
IA [auth i],
JA [auth j],
LA [auth l],
PA [auth p],
TA [auth t],
UA [auth u],
Y,
YA [auth y],
ZA [auth z]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BB [auth 1],
CA [auth c],
CB [auth 2],
DA [auth d],
AA [auth a],
BB [auth 1],
CA [auth c],
CB [auth 2],
DA [auth d],
EB [auth 4],
FA [auth f],
OA [auth o],
QA [auth q],
RA [auth r],
SA [auth s],
VA [auth v],
WA [auth w],
XA [auth x],
Z
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseBA [auth b],
HA [auth h],
KA [auth k],
NA [auth n]
5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e],
GA [auth g],
MA [auth m]
4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 318.123α = 90
b = 187.167β = 90.47
c = 353.636γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary