+Open data
-Basic information
Entry | Database: PDB / ID: 5gka | |||||||||
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Title | cryo-EM structure of human Aichi virus | |||||||||
Components |
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Keywords | VIRUS / Picornavirus / entry / receptor binding / gastroenteritis | |||||||||
Function / homology | Function and homology information host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell ...host cell Golgi membrane / symbiont-mediated suppression of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / 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 Similarity search - Function | |||||||||
Biological species | Aichi virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zhu, L. / Wang, X.X. / Ren, J.S. / Tuthill, T.J. / Fry, E.E. / Rao, Z.H. / Stuart, D.I. | |||||||||
Funding support | China, United Kingdom, 2items
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Citation | Journal: Nat Microbiol / Year: 2016 Title: Structure of human Aichi virus and implications for receptor binding. Authors: Ling Zhu / Xiangxi Wang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Shuai Yuan / Teruo Yamashita / Tobias J Tuthill / Elizabeth E Fry / Zihe Rao / David I Stuart / Abstract: Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially ...Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially in developing countries. The seroprevalence of AiV is approximately 60% in children under the age of ten years and reaches 90% later in life. There is no available vaccine or effective antiviral treatment. Here, we describe the structure of AiV at 3.7 Å. This first high-resolution structure for a kobuvirus is intermediate between those of the enteroviruses and cardioviruses, with a shallow, narrow depression bounded by the prominent VP0 CD loops (linking the C and D strands of the β-barrel), replacing the depression known as the canyon, frequently the site of receptor attachment in enteroviruses. VP0 is not cleaved to form VP2 and VP4, so the 'VP2' β-barrel structure is complemented with a unique extended structure on the inside of the capsid. On the outer surface, a polyproline helix structure, not seen previously in picornaviruses is present at the C terminus of VP1, a position where integrin binding motifs are found in some other picornaviruses. A peptide corresponding to this polyproline motif somewhat attenuates virus infectivity, presumably blocking host-cell attachment. This may guide cellular receptor identification. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 5gka.cif.gz | 160.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gka.ent.gz | 124.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gka_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5gka_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5gka_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5gka_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gka ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gka | HTTPS FTP |
-Related structure data
Related structure data | 9517MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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