7T3D

CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Broadly neutralizing antibodies target a haemagglutinin anchor epitope.

Guthmiller, J.J.Han, J.Utset, H.A.Li, L.Lan, L.Y.Henry, C.Stamper, C.T.McMahon, M.O'Dell, G.Fernandez-Quintero, M.L.Freyn, A.W.Amanat, F.Stovicek, O.Gentles, L.Richey, S.T.de la Pena, A.T.Rosado, V.Dugan, H.L.Zheng, N.Y.Tepora, M.E.Bitar, D.J.Changrob, S.Strohmeier, S.Huang, M.Garcia-Sastre, A.Liedl, K.R.Bloom, J.D.Nachbagauer, R.Palese, P.Krammer, F.Coughlan, L.Ward, A.B.Wilson, P.C.

(2022) Nature 602: 314-320

  • DOI: https://doi.org/10.1038/s41586-021-04356-8
  • Primary Citation of Related Structures:  
    7T3D

  • PubMed Abstract: 

    Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection 1 . However, viral mutants that escape broadly neutralizing antibodies have been reported 2,3 . The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine 4,5 , which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.


  • Organizational Affiliation

    Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, USA. jguthmiller@uchicago.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA,
G [auth E],
M [auth F]
331Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S1 
Go to UniProtKB:  C3W5S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S1
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB,
H [auth G],
N [auth I]
174Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 1 
Gene Names: HA
UniProt
Find proteins for C3W5S1 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S1 
Go to UniProtKB:  C3W5S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
2B05 mAb light chainC [auth D],
I [auth M],
O [auth N]
107Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
2B05 mAb heavy chainD [auth C],
J,
P [auth K]
120Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
222-1C06 mAb heavy chainE [auth H],
K [auth O],
Q [auth P]
122Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
222-1C06 mAb light chainF [auth L],
L [auth Q],
R
108Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
S, T, U
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
EA [auth G]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth G],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth F],
JA [auth I],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93019C00051

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Data processing
  • Version 1.3: 2024-10-30
    Changes: Data collection, Structure summary