9N8P | pdb_00009n8p

Subtomogram average of dimers of influenza HA trimers


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryoelectron tomography.

Huang, Q.J.Kim, R.Song, K.Grigorieff, N.Munro, J.B.Schiffer, C.A.Somasundaran, M.

(2025) Proc Natl Acad Sci U S A 122: e2426427122-e2426427122

  • DOI: https://doi.org/10.1073/pnas.2426427122
  • Primary Citation of Related Structures:  
    9N8P

  • PubMed Abstract: 

    Influenza viruses are enveloped, negative-sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80 to 90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of purified receptor-free and receptor-bound HA, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryoelectron tomography to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even interglycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and the formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8 to 10 Å reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin
A, C, E, G, I
A, C, E, G, I, K
327Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F, H, J
B, D, F, H, J, L
160Influenza A virus (A/Puerto Rico/8/1934(H1N1))Mutation(s): 0 
UniProt
Find proteins for P03452 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
Explore P03452 
Go to UniProtKB:  P03452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03452
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose
M [auth S],
N [auth U],
O [auth T],
P [auth N],
Q [auth M],
M [auth S],
N [auth U],
O [auth T],
P [auth N],
Q [auth M],
R [auth O]
2N/A
Glycosylation Resources
GlyTouCan:  G63069TR
GlyCosmos:  G63069TR
GlyGen:  G63069TR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM143773
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM151996

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Database references