6ONA

Crystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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This is version 2.2 of the entry. See complete history


Literature

Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.

Ghafoori, S.M.Petersen, G.F.Conrady, D.G.Calhoun, B.M.Stigliano, M.Z.Z.Baydo, R.O.Grice, R.Abendroth, J.Lorimer, D.D.Edwards, T.E.Forwood, J.K.

(2023) Sci Rep 13: 6940-6940

  • DOI: https://doi.org/10.1038/s41598-023-33529-w
  • Primary Citation of Related Structures:  
    6D8W, 6ML8, 6MYA, 6N41, 6ONA, 6OSR, 7JP4, 7JPD

  • PubMed Abstract: 

    Influenza virus (IV) causes several outbreaks of the flu each year resulting in an economic burden to the healthcare system in the billions of dollars. Several influenza pandemics have occurred during the last century and estimated to have caused 100 million deaths. There are four genera of IV, A (IVA), B (IVB), C (IVC), and D (IVD), with IVA being the most virulent to the human population. Hemagglutinin (HA) is an IVA surface protein that allows the virus to attach to host cell receptors and enter the cell. Here we have characterised the high-resolution structures of seven IVA HAs, with one in complex with the anti-influenza head-binding antibody C05. Our analysis revealed conserved receptor binding residues in all structures, as seen in previously characterised IV HAs. Amino acid conservation is more prevalent on the stalk than the receptor binding domain (RBD; also called the head domain), allowing the virus to escape from antibodies targeting the RBD. The equivalent site of C05 antibody binding to A/Denver/57 HA appears hypervariable in the other H1N1 IV HAs. Modifications within this region appear to disrupt binding of the C05 antibody, as these HAs no longer bind the C05 antibody by analytical SEC. Our study brings new insights into the structural and functional recognition of IV HA proteins and can contribute to further development of anti-influenza vaccines.


  • Organizational Affiliation

    School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2650, Australia. jforwood@csu.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, B, C
538Influenza A virus (A/Hickox/1940(H1N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q0HD60 (Influenza A virus (strain A/Hickox/1940 H1N1))
Explore Q0HD60 
Go to UniProtKB:  Q0HD60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0HD60
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
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
D, E
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
FA [auth C]
H [auth A]
I [auth A]
J [auth A]
P [auth B]
FA [auth C],
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
K [auth A]
L [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
K [auth A],
L [auth A],
T [auth B],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth C]
EA [auth C]
M [auth A]
N [auth A]
O [auth A]
DA [auth C],
EA [auth C],
M [auth A],
N [auth A],
O [auth A],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.56α = 90
b = 102.25β = 91.07
c = 160.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-05-24
    Changes: Database references, Structure summary
  • Version 2.2: 2023-10-25
    Changes: Data collection, Refinement description