8ZDW | pdb_00008zdw

The cryoEM structure of H5N1 HA split from symmetric filament in conformation A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites.

Li, R.Gao, J.Wang, L.Gui, M.Xiang, Y.

(2024) Npj Viruses 2: 48-48

  • DOI: https://doi.org/10.1038/s44298-024-00059-9
  • Primary Citation of Related Structures:  
    8ZDV, 8ZDW

  • PubMed Abstract: 

    The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza viruses. We find that the H5N1 HA can form filaments that comprise two head-to-head HA trimers. Multivalent interactions between the two HA trimers are mediated by glycans attached to N158. The distal Sia1-Gal2-NAG3 sugar moiety of N158 interacts with the receptor binding site on the opposing HA trimer. Additional interactions are observed between NAG3 and residues K222 and K193. The H5N8 HA lacks the N158 glycosylation site and does not form the filamentous structure. However, the H5N8 HA exhibits an auto-inhibition conformation, where the receptor binding site is occupied by the glycan chain attached to residue N169 from a neighboring protomer. These structures represent native HA-glycan interactions, which may closely mimic the receptor-HA interactions on the cell surface.


  • Organizational Affiliation
    • Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, 100084, Beijing, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininA,
K [auth C],
L [auth H]
337Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1))
Explore Q6DQ33 
Go to UniProtKB:  Q6DQ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ33
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininB,
E [auth D],
F [auth I]
228Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1))
Explore Q6DQ33 
Go to UniProtKB:  Q6DQ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DQ33
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H5M9 Fab, light chainC [auth R],
I [auth E],
J
217Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chainD [auth U],
G [auth F],
H [auth L]
222Mus musculusMutation(s): 0 
UniProt
Find proteins for U5LP42 (Mus musculus)
Explore U5LP42 
Go to UniProtKB:  U5LP42
Entity Groups  
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UniProt GroupU5LP42
Sequence Annotations
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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-glucopyranoseM [auth G],
P [auth N],
S [auth Q]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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
N [auth K],
O [auth M],
Q [auth O],
R [auth P],
T [auth S],
N [auth K],
O [auth M],
Q [auth O],
R [auth P],
T [auth S],
U [auth T]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
V, W, X
3N/A
Glycosylation Resources
GlyTouCan:  G00065MO
GlyCosmos:  G00065MO
GlyGen:  G00065MO
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 B]
BA [auth R]
CA [auth D]
DA [auth I]
EA [auth E]
AA [auth B],
BA [auth R],
CA [auth D],
DA [auth I],
EA [auth E],
FA [auth J],
GA [auth C],
HA [auth C],
IA [auth H],
JA [auth H],
Y [auth A],
Z [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-14
    Changes: Data collection, Database references
  • Version 1.4: 2025-07-23
    Changes: Data collection