5I08

Prefusion structure of a human coronavirus spike protein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Pre-fusion structure of a human coronavirus spike protein.

Kirchdoerfer, R.N.Cottrell, C.A.Wang, N.Pallesen, J.Yassine, H.M.Turner, H.L.Corbett, K.S.Graham, B.S.McLellan, J.S.Ward, A.B.

(2016) Nature 531: 118-121

  • DOI: 10.1038/nature17200

  • PubMed Abstract: 
  • HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in pa ...

    HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in part by the coronavirus spike (S) protein, which binds cellular receptors and mediates membrane fusion. As the largest known class I fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. Here we present the 4.0 Å resolution structure of the trimeric HKU1 S protein determined using single-particle cryo-electron microscopy. In the pre-fusion conformation, the receptor-binding subunits, S1, rest above the fusion-mediating subunits, S2, preventing their conformational rearrangement. Surprisingly, the S1 C-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. These features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive S protein destabilization through receptor binding and proteolytic cleavage. These studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.,Viral Pathogenesis Laboratory, National Institute of Allergy and Infectious Diseases, Building 40, Room 2502, 40 Convent Drive, Bethesda, Maryland 20892, USA.,Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein, envelope glycoprotein chimera
A, B, C
1299Human immunodeficiency virus 1Human coronavirus HKU1 (isolate N5)
This entity is chimeric
Mutation(s): 5 
Gene Names: S
Find proteins for M1E1E4 (Human immunodeficiency virus 1)
Go to UniProtKB:  M1E1E4
Find proteins for Q0ZME7 (Human coronavirus HKU1 (isolate N5))
Go to UniProtKB:  Q0ZME7
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2016-04-13
    Type: Database references
  • Version 1.3: 2019-12-18
    Type: Other