5K0U

CryoEM structure of the full virion of a human rhinovirus C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.5 of the entry. See complete history


Literature

Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma.

Liu, Y.Hill, M.G.Klose, T.Chen, Z.Watters, K.Bochkov, Y.A.Jiang, W.Palmenberg, A.C.Rossmann, M.G.

(2016) Proc Natl Acad Sci U S A 113: 8997-9002

  • DOI: https://doi.org/10.1073/pnas.1606595113
  • Primary Citation of Related Structures:  
    5JZG, 5K0U

  • PubMed Abstract: 

    Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1279Rhinovirus CMutation(s): 1 
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D8F2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP3235Rhinovirus CMutation(s): 0 
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D8F2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP2265Rhinovirus CMutation(s): 0 
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D8F2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP466Rhinovirus CMutation(s): 0 
UniProt
Find proteins for E5D8F2 (Human rhinovirus C (strain C15))
Explore E5D8F2 
Go to UniProtKB:  E5D8F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE5D8F2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10.1-2155
MODEL REFINEMENTCoot0.8.2
RECONSTRUCTIONjspr

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI011219
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI104317

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-06
    Changes: Data collection, Database references, Derived calculations