5A8F

Structure and genome release mechanism of human cardiovirus Saffold virus-3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure and Genome Release Mechanism of Human Cardiovirus Saffold Virus-3.

Mullapudi, E.Novacek, J.Palkova, L.Kulich, P.Lindberg, A.M.Van Kuppeveld, F.J.M.Plevka, P.

(2016) J Virol 90: 7628

  • DOI: 10.1128/JVI.00746-16
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address t ...

    In order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the family Picornaviridae SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an "altered" particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.


    Organizational Affiliation

    Central European Institute of Technology, Masaryk University, Brno, Czech Republic pavel.plevka@muni.ceitec.cz.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN SAFFOLD VIRUS-3 VP1A219Saffold virusMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for C0MHL9 (Saffold virus)
Explore C0MHL9 
Go to UniProtKB:  C0MHL9
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GENOME POLYPHUMAN SAFFOLD VIRUS-3 VP3 PROTEINB189Saffold virusMutation(s): 0 
Find proteins for E3TMG9 (Saffold virus)
Explore E3TMG9 
Go to UniProtKB:  E3TMG9
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HUMAN SAFFOLD VIRUS-3 VP2C258Saffold virusMutation(s): 0 
EC: 3.6.4.13 (UniProt), 3.4.22.28 (UniProt), 2.7.7.48 (UniProt)
Find proteins for C0MHL9 (Saffold virus)
Explore C0MHL9 
Go to UniProtKB:  C0MHL9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-22
    Changes: Database references
  • Version 1.2: 2016-08-31
    Changes: Database references
  • Version 1.3: 2017-08-30
    Changes: Data collection
  • Version 1.4: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations