+Open data
-Basic information
Entry | Database: PDB / ID: 5cfc | ||||||
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Title | Crystal Structure of Human Cardiovirus SAFV-3 | ||||||
Components |
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Keywords | VIRUS / Virion / capsid / saffold virus / pathogen | ||||||
Function / homology | Function and homology information icosahedral viral capsid / RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : ...icosahedral viral capsid / RNA-protein covalent cross-linking / : / host cell nucleolus / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saffold virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Mullapudi, E. / Plevka, P. | ||||||
Citation | Journal: J Virol / Year: 2016 Title: Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3. Authors: Edukondalu Mullapudi / Jiří Nováček / Lenka Pálková / Pavel Kulich / A Michael Lindberg / Frank J M van Kuppeveld / Pavel Plevka / 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 ...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. IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from ...IMPORTANCE: A capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release of Human Saffold virus 3 Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cfc.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cfc.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 5cfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/5cfc ftp://data.pdbj.org/pub/pdb/validation_reports/cf/5cfc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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