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Yorodumi- PDB-5g52: Crystallographic structure of full particle of Deformed Wing Virus -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g52 | ||||||
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Title | Crystallographic structure of full particle of Deformed Wing Virus | ||||||
Components |
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Keywords | VIRUS / PICORNAVIRALES / IFLAVIRIDAE / IFLAVIRUS / DWV CAPSID / P JELLYROLL / CATALYTIC SITE PROTEASE / LIPASE ESTERASE RECEPTO | ||||||
Function / homology | Function and homology information host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis ...host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | DEFORMED WING VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.802 Å | ||||||
Authors | Skubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structure of deformed wing virus, a major honey bee pathogen. Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka / Abstract: The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) ...The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family , together with its vector, the mite , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g52.cif.gz | 185.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g52.ent.gz | 151.7 KB | Display | PDB format |
PDBx/mmJSON format | 5g52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/5g52 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/5g52 | HTTPS FTP |
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-Related structure data
Related structure data | 3570C 3574C 3575C 4009C 4014C 5g51C 5l7qC 5l8qC 5mupC 5mv5C 5mv6C C: citing same article (ref.) |
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Similar structure data |
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-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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