9DWE | pdb_00009dwe

Cryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex with LSTa and antibody CR9114


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth.

Good, M.R.Fernandez-Quintero, M.L.Ji, W.Rodriguez, A.J.Han, J.Ward, A.B.Guthmiller, J.J.

(2024) Nat Commun 15: 10768-10768

  • DOI: https://doi.org/10.1038/s41467-024-54934-3
  • Primary Citation of Related Structures:  
    9DWE

  • PubMed Abstract: 

    Clade 2.3.4.4b H5N1 is causing an unprecedented outbreak in dairy cows in the United States. To understand if recent H5N1 viruses are changing their receptor use, we screened recombinant hemagglutinin (HA) from historical and recent 2.3.4.4b H5N1 viruses for binding to distinct glycans bearing terminal sialic acids using a glycan microarray. We find that H5 from A/Texas/37/2024, an isolate from the dairy cow outbreak, has increased binding breadth to core glycans bearing terminal α2,3 sialic acids, the avian receptor, compared to historical and recent 2.3.4.4b H5N1 viruses. We do not observe any binding to α2,6 sialic acids, the receptor used by human seasonal influenza viruses. Using molecular dynamics and a cryo-EM structure of A/Texas/37/2024 H5, we show A/Texas/37/2024 H5 is more flexible within the receptor-binding site compared to a 2.3.4.4b H5 from 2022. We identify a single mutation outside of the receptor binding site, T199I, is responsible for increased binding breadth, as it increases receptor binding site flexibility. Together, these data show recent H5N1 viruses are evolving increased receptor binding breadth which could impact the host range and cell types infected with H5N1.


  • Organizational Affiliation
    • Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CR9114 Fab light chainA [auth L],
D [auth M],
G [auth N]
110Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CR9114 Fab Fab heavy chainB [auth H],
E [auth I],
H [auth J]
120Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininC [auth A],
F [auth B],
I [auth C]
572Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8E4ZAK5 (Influenza A virus)
Explore A0A8E4ZAK5 
Go to UniProtKB:  A0A8E4ZAK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8E4ZAK5
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranoseJ [auth P],
K [auth D],
L [auth E]
2N/A
Glycosylation Resources
GlyTouCan:  G30207PZ
GlyCosmos:  G30207PZ
GlyGen:  G30207PZ
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
AA [auth C],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv.4.5.3
MODEL REFINEMENTPHENIX

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: 2024-12-04
    Type: Initial release
  • Version 2.0: 2024-12-18
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2025-01-15
    Changes: Data collection, Database references