3WHE

A new conserved neutralizing epitope at the globular head of hemagglutinin in H3N2 influenza viruses

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Conserved Neutralizing Epitope at Globular Head of Hemagglutinin in H3N2 Influenza Viruses.

Iba, Y., Fujii, Y., Ohshima, N., Sumida, T., Kubota-Koketsu, R., Ikeda, M., Wakiyama, M., Shirouzu, M., Okada, J., Okuno, Y., Kurosawa, Y., Yokoyama, S.

(2014) J Virol 

  • DOI: 10.1128/JVI.00420-14
  • Primary Citation of Related Structures:  
    3WHE

  • PubMed Abstract: 

    • Neutralizing antibodies that target the hemagglutinin of influenza virus either inhibit binding of hemagglutinin to cellular receptors or prevent the low-pH-induced conformational change in hemagglutinin required for membrane fusion. In general, the former type of antibody binds to the globular head formed by HA1 and has narrow strain specificity, while the latter type binds to the stem mainly formed by HA2 and has broad strain specificity ...

    Neutralizing antibodies that target the hemagglutinin of influenza virus either inhibit binding of hemagglutinin to cellular receptors or prevent the low-pH-induced conformational change in hemagglutinin required for membrane fusion. In general, the former type of antibody binds to the globular head formed by HA1 and has narrow strain specificity, while the latter type binds to the stem mainly formed by HA2 and has broad strain specificity. In the present study, we analyzed the epitope and function of a broadly neutralizing human antibody against H3N2 viruses, F005-126. The crystal structure of F005-126 Fab in complex with hemagglutinin revealed that the antibody binds to the globular head, spans a cleft formed by two hemagglutinin monomers in a hemagglutinin trimer, and cross-links them. It recognizes two peptide portions (sites L and R) and a glycan linked to asparagine at residue 285 using three complementarity-determining regions and framework 3 in the heavy chain. Binding of the antibody to sites L (residues 171 to 173, 239, and 240) and R (residues 91, 92, 270 to 273, 284, and 285) is mediated mainly by van der Waals contacts with the main chains of the peptides in these sites and secondarily by hydrogen bonds with a few side chains of conserved sequences in HA1. Furthermore, the glycan recognized by F005-126 is conserved among H3N2 viruses. F005-126 has the ability to prevent low-pH-induced conformational changes in hemagglutinin. The newly identified conserved epitope, including the glycan, should be immunogenic in humans and may induce production of broadly neutralizing antibodies against H3 viruses.

    Organizational Affiliation: 

    RIKEN Systems and Structural Biology Center, Suehiro, Tsurumi, Yokohama, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemagglutinin
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
493Influenza A virus (A/Aichi/2-1/1968(H3N2))Mutation(s): 0 
Gene Names: 126567434, HA
UniProt
Find proteins for T2HNI1 (Influenza A virus)
Explore T2HNI1 
Go to UniProtKB:  T2HNI1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin heavy chain226Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
immunoglobulin light chain220Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-glucopyranose
CB [auth s], FB [auth v], IB [auth y], KA [auth a], LB [auth BA], NA [auth d], OB [auth EA], QA [auth g]
CB [auth s], FB [auth v], IB [auth y], KA [auth a], LB [auth BA], NA [auth d], OB [auth EA], QA [auth g], RB [auth HA], TA [auth j], WA [auth m], ZA [auth p]
7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranose
AB [auth q], DB [auth t], GB [auth w], JB [auth z], LA [auth b], MB [auth CA], OA [auth e], PB [auth FA]
AB [auth q], DB [auth t], GB [auth w], JB [auth z], LA [auth b], MB [auth CA], OA [auth e], PB [auth FA], RA [auth h], SB [auth IA], UA [auth k], XA [auth n]
6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 6
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
BB [auth r], EB [auth u], HB [auth x], KB [auth AA], MA [auth c], NB [auth DA], PA [auth f], QB [auth GA]
BB [auth r], EB [auth u], HB [auth x], KB [auth AA], MA [auth c], NB [auth DA], PA [auth f], QB [auth GA], SA [auth i], TB [auth JA], VA [auth l], YA [auth o]
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AC [auth D] , BC [auth D] , CC [auth E] , DC [auth E] , EC [auth F] , FC [auth F] , GC [auth G] , HC [auth G] , 
AC [auth D],  BC [auth D],  CC [auth E],  DC [auth E],  EC [auth F],  FC [auth F],  GC [auth G],  HC [auth G],  IC [auth H],  JC [auth H],  KC [auth I],  LC [auth I],  MC [auth J],  NC [auth J],  OC [auth K],  PC [auth K],  QC [auth L],  RC [auth L],  UB [auth A],  VB [auth A],  WB [auth B],  XB [auth B],  YB [auth C],  ZB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 391.037α = 90
b = 241.173β = 123.62
c = 223.214γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHASESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Derived calculations
  • Version 1.2: 2020-03-04
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary