7SCO

Structure of H1 influenza hemagglutinin bound to Fab 310-39G10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus.

Sangesland, M.Torrents de la Pena, A.Boyoglu-Barnum, S.Ronsard, L.Mohamed, F.A.N.Moreno, T.B.Barnes, R.M.Rohrer, D.Lonberg, N.Ghebremichael, M.Kanekiyo, M.Ward, A.Lingwood, D.

(2022) Immunity 55: 1693-1709.e8

  • DOI: https://doi.org/10.1016/j.immuni.2022.07.006
  • Primary Citation of Related Structures:  
    7SCN, 7SCO

  • PubMed Abstract: 

    Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrated that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage expandability, we compared F54 versus L54 as substrate within humanized mice, where antibodies develop with human-like CDRH3 diversity but are restricted to single V H genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. Therefore, IGHV1-69 polymorphism, which is skewed ethnically, gates tolerance and vaccine expandability of influenza bnAbs.


  • Organizational Affiliation

    The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA,
E [auth C],
I [auth G]
322Influenza A virus (A/South Canterbury/35/2000(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q289M7 (Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1))
Explore Q289M7 
Go to UniProtKB:  Q289M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ289M7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB,
F [auth D],
J [auth I]
231Influenza A virus (A/South Canterbury/35/2000(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q289M7 (Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1))
Explore Q289M7 
Go to UniProtKB:  Q289M7
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ289M7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
310-39G10 Fab, Heavy ChainC [auth H],
G [auth E],
K [auth J]
119Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
310-39G10 Fab, Light ChainD [auth L],
H [auth F],
L [auth K]
108Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N, O
2N/AN-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 G]
P [auth A]
Q [auth A]
R [auth A]
S [auth A]
AA [auth G],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth G],
Y [auth G],
Z [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1170236
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2022-09-28
    Changes: Database references