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 2.2 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 88: 7130-7144

  • DOI: https://doi.org/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. 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

    Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, B, C, D, E
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: 126567434HA
UniProt
Find proteins for T2HNI1 (Influenza A virus)
Explore T2HNI1 
Go to UniProtKB:  T2HNI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2HNI1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin heavy chain226Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin light chain220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D 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],
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
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D 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],
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
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Entity ID: 6
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
BB [auth r],
EB [auth u],
HB [auth x],
KB [auth AA],
MA [auth c],
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
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / 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]
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
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

View Full Validation Report



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
  • Version 2.1: 2022-08-24
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-11-08
    Changes: Data collection, Refinement description