6Y5I

Dilated form 1 of X-31 Influenza Haemagglutinin at pH 5 (State II)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.0 of the entry. See complete history


Literature

Structural transitions in influenza haemagglutinin at membrane fusion pH.

Benton, D.J.Gamblin, S.J.Rosenthal, P.B.Skehel, J.J.

(2020) Nature 583: 150-153

  • DOI: https://doi.org/10.1038/s41586-020-2333-6
  • Primary Citation of Related Structures:  
    6Y5G, 6Y5H, 6Y5I, 6Y5J, 6Y5K, 6Y5L

  • PubMed Abstract: 

    Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface receptors and mediate membrane fusion. In the case of influenza, the receptor-binding glycoprotein is the haemagglutinin (HA), and following receptor-mediated uptake of the bound virus by endocytosis 1 , it is the HA that mediates fusion of the virus envelope with the membrane of the endosome 2 . Each subunit of the trimeric HA consists of two disulfide-linked polypeptides, HA1 and HA2. The larger, virus-membrane-distal, HA1 mediates receptor binding; the smaller, membrane-proximal, HA2 anchors HA in the envelope and contains the fusion peptide, a region that is directly involved in membrane interaction 3 . The low pH of endosomes activates fusion by facilitating irreversible conformational changes in the glycoprotein. The structures of the initial HA at neutral pH and the final HA at fusion pH have been investigated by electron microscopy 4,5 and X-ray crystallography 6-8 . Here, to further study the process of fusion, we incubate HA for different times at pH 5.0 and directly image structural changes using single-particle cryo-electron microscopy. We describe three distinct, previously undescribed forms of HA, most notably a 150 Å-long triple-helical coil of HA2, which may bridge between the viral and endosomal membranes. Comparison of these structures reveals concerted conformational rearrangements through which the HA mediates membrane fusion.


  • Organizational Affiliation

    Structural Biology of Disease Processes Laboratory, Francis Crick Institute, London, UK. donald.benton@crick.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
X-31 Influenza Haemagglutinin HA1A,
E,
F [auth C]
318unidentified influenza virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03437
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
X-31 Influenza Haemagglutinin HA2B,
C [auth D],
D [auth F]
172unidentified influenza virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2))
Explore P03437 
Go to UniProtKB:  P03437
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03437
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
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
G, L, N
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, I, J, K, M
H, I, J, K, M, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001078
The Francis Crick InstituteUnited KingdomFC001143

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary