6SK6

Cryo-EM structure of rhinovirus-B5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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

Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site.

Wald, J.Pasin, M.Richter, M.Walther, C.Mathai, N.Kirchmair, J.Makarov, V.A.Goessweiner-Mohr, N.Marlovits, T.C.Zanella, I.Real-Hohn, A.Verdaguer, N.Blaas, D.Schmidtke, M.

(2019) Proc.Natl.Acad.Sci.USA 116: 19109-19115

  • DOI: 10.1073/pnas.1904732116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 (VP1). In resistant RVs and EVs, bulky residues in ...

    Viral inhibitors, such as pleconaril and vapendavir, target conserved regions in the capsids of rhinoviruses (RVs) and enteroviruses (EVs) by binding to a hydrophobic pocket in viral capsid protein 1 (VP1). In resistant RVs and EVs, bulky residues in this pocket prevent their binding. However, recently developed pyrazolopyrimidines inhibit pleconaril-resistant RVs and EVs, and computational modeling has suggested that they also bind to the hydrophobic pocket in VP1. We studied the mechanism of inhibition of pleconaril-resistant RVs using RV-B5 (1 of the 7 naturally pleconaril-resistant rhinoviruses) and OBR-5-340, a bioavailable pyrazolopyrimidine with proven in vivo activity, and determined the 3D-structure of the protein-ligand complex to 3.6 Å with cryoelectron microscopy. Our data indicate that, similar to other capsid binders, OBR-5-340 induces thermostability and inhibits viral adsorption and uncoating. However, we found that OBR-5-340 attaches closer to the entrance of the pocket than most other capsid binders, whose viral complexes have been studied so far, showing only marginal overlaps of the attachment sites. Comparing the experimentally determined 3D structure with the control, RV-B5 incubated with solvent only and determined to 3.2 Å, revealed no gross conformational changes upon OBR-5-340 binding. The pocket of the naturally OBR-5-340-resistant RV-A89 likewise incubated with OBR-5-340 and solved to 2.9 Å was empty. Pyrazolopyrimidines have a rigid molecular scaffold and may thus be less affected by a loss of entropy upon binding. They interact with less-conserved regions than known capsid binders. Overall, pyrazolopyrimidines could be more suitable for the development of new, broadly active inhibitors.


    Organizational Affiliation

    Institute for Structural and Systems Biology, University Medical Center Hamburg-Eppendorf, D-22607 Hamburg, Germany.,Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital, D-07740 Jena, Germany.,Institute of Biophysics, Johannes Kepler University Linz, A-4020 Linz, Austria.,Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, A-1030 Vienna, Austria.,Center for Bioinformatics (ZBH), Universität Hamburg, D-20146 Hamburg, Germany.,Structural Biology Unit, Institute of Molecular Biology of Barcelona, Spanish Research Council, E-08028 Barcelona, Spain.,German Electron Synchrotron Centre (DESY), D-22607 Hamburg, Germany.,Department of Medical Microbiology, Section of Experimental Virology, Jena University Hospital, D-07740 Jena, Germany; dieter.blaas@meduniwien.ac.at michaela.schmidtke@med.uni-jena.de.,Department of Chemistry, University of Bergen, N-5020 Bergen, Norway.,Computational Biology Unit (CBU), University of Bergen, N-5020 Bergen, Norway.,Centre for Structural Systems Biology (CSSB), D-22607 Hamburg, Germany.,Laboratory of Biomedicinal Chemistry, Institute of Biochemistry, Federal Research Center Fundamentals of Biotechnology Russian Academy of Sciences, 119071 Moscow, Russia.,Department of Medical Biochemistry, Max F. Perutz Laboratories, Vienna Biocenter, Medical University of Vienna, A-1030 Vienna, Austria; dieter.blaas@meduniwien.ac.at michaela.schmidtke@med.uni-jena.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rhinovirus B5 VP4
D
69Human rhinovirus B5Mutation(s): 0 
Find proteins for Q80SQ3 (Human rhinovirus B5)
Go to UniProtKB:  Q80SQ3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rhinovirus B5 VP2
B
252Human rhinovirus B5Mutation(s): 0 
Find proteins for B9V433 (Human rhinovirus B5)
Go to UniProtKB:  B9V433
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Rhinovirus B5 VP1
A
288Human rhinovirus B5Mutation(s): 0 
Find proteins for Q7T659 (Human rhinovirus B5)
Go to UniProtKB:  Q7T659
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Rhinovirus B5 VP3
C
231Human rhinovirus B5Mutation(s): 0 
Find proteins for B9V433 (Human rhinovirus B5)
Go to UniProtKB:  B9V433
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionAustria653706

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references
  • Version 1.2: 2019-09-25
    Type: Data collection, Database references
  • Version 1.3: 2019-10-02
    Type: Data collection, Derived calculations