8ZDV | pdb_00008zdv

The cryoEM structure of H5N8 HA in an auto inhibited state


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininA [auth B],
B [auth A],
C
336Influenza 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: 4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HemagglutininD [auth G],
E [auth H],
F [auth I]
190Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A8K1DYS3 (Influenza A virus)
Explore A0A8K1DYS3 
Go to UniProtKB:  A0A8K1DYS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8K1DYS3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D],
H [auth E],
I [auth F]
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G85526ZL
GlyCosmos:  G85526ZL
GlyGen:  G85526ZL
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 
J [auth B]
K [auth B]
L [auth B]
M [auth A]
N [auth A]
J [auth B],
K [auth B],
L [auth B],
M [auth A],
N [auth A],
O [auth A],
P [auth C],
Q [auth C],
R [auth C],
S [auth G],
T [auth H],
U [auth I]
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
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2024-11-20
    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: 2025-07-16
    Changes: Data collection