+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4112 | |||||||||
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Title | Aichi virus 1: empty particle | |||||||||
Map data | Archie Virus 1: Empty particle | |||||||||
Sample | Aichi != Aichi virus 1 Aichi
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Keywords | picornavirus / picornaviridae / Aichi virus 1 / empty particle / kobuvirus / 50 genome / release / human / pathogen / virus / RNA | |||||||||
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 / symbiont-mediated suppression of host gene expression / monoatomic ion channel activity / RNA helicase activity / RNA helicase ...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 / symbiont-mediated suppression of host gene expression / monoatomic ion channel activity / 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 Similarity search - Function | |||||||||
Biological species | Aichi virus / Aichi virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Sabin C / Fuzik T | |||||||||
Citation | Journal: J Virol / Year: 2016 Title: Structure of Aichi Virus 1 and Its Empty Particle: Clues to Kobuvirus Genome Release Mechanism. Authors: Charles Sabin / Tibor Füzik / Karel Škubník / Lenka Pálková / A Michael Lindberg / Pavel Plevka / Abstract: (AiV-1) is a human pathogen from the genus of the family. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. ... (AiV-1) is a human pathogen from the genus of the family. Worldwide, 80 to 95% of adults have antibodies against the virus. AiV-1 infections are associated with nausea, gastroenteritis, and fever. Unlike most picornaviruses, kobuvirus capsids are composed of only three types of subunits: VP0, VP1, and VP3. We present here the structure of the AiV-1 virion determined to a resolution of 2.1 Å using X-ray crystallography. The surface loop puff of VP0 and knob of VP3 in AiV-1 are shorter than those in other picornaviruses. Instead, the 42-residue BC loop of VP0 forms the most prominent surface feature of the AiV-1 virion. We determined the structure of AiV-1 empty particle to a resolution of 4.2 Å using cryo-electron microscopy. The empty capsids are expanded relative to the native virus. The N-terminal arms of capsid proteins VP0, which mediate contacts between the pentamers of capsid protein protomers in the native AiV-1 virion, are disordered in the empty capsid. Nevertheless, the empty particles are stable, at least , and do not contain pores that might serve as channels for genome release. Therefore, extensive and probably reversible local reorganization of AiV-1 capsid is required for its genome release. Aichi virus 1 (AiV-1) is a human pathogen that can cause diarrhea, abdominal pain, nausea, vomiting, and fever. AiV-1 is identified in environmental screening studies with higher frequency and greater abundance than other human enteric viruses. Accordingly, 80 to 95% of adults worldwide have suffered from AiV-1 infections. We determined the structure of the AiV-1 virion. Based on the structure, we show that antiviral compounds that were developed against related enteroviruses are unlikely to be effective against AiV-1. The surface of the AiV-1 virion has a unique topology distinct from other related viruses from the family. We also determined that AiV-1 capsids form compact shells even after genome release. Therefore, AiV-1 genome release requires large localized and probably reversible reorganization of the capsid. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4112.map.gz | 8.8 MB | EMDB map data format | |
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Header (meta data) | emd-4112-v30.xml emd-4112.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4112_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_4112.png | 170.7 KB | ||
Filedesc metadata | emd-4112.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4112 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4112 | HTTPS FTP |
-Validation report
Summary document | emd_4112_validation.pdf.gz | 291.7 KB | Display | EMDB validaton report |
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Full document | emd_4112_full_validation.pdf.gz | 290.9 KB | Display | |
Data in XML | emd_4112_validation.xml.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4112 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4112 | HTTPS FTP |
-Related structure data
Related structure data | 5lvcMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4112.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Archie Virus 1: Empty particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.73 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Aichi
Entire | Name: Aichi |
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Components |
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-Supramolecule #1: Aichi virus 1
Supramolecule | Name: Aichi virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1313215 / Sci species name: Aichi virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus |
Molecular weight | Theoretical: 27.194688 KDa |
Recombinant expression | Organism: Chlorocebus sabaeus (green monkey) |
Sequence | String: TLTEDLDAPQ DTGNIENGAA DNSPQPRTTF DYTGNPLPPD TKLENFFSFY RLLPMGGSGA PSLSFPADEG TIIPLNPINW LKGADVSGI AAMLSCFTYI AADLRITLRF SNPNDNPATM LVAFAPPGAT IPLKPTRQML SNFYMAEVPV SAATSTMVSF S IPYTSPLS ...String: TLTEDLDAPQ DTGNIENGAA DNSPQPRTTF DYTGNPLPPD TKLENFFSFY RLLPMGGSGA PSLSFPADEG TIIPLNPINW LKGADVSGI AAMLSCFTYI AADLRITLRF SNPNDNPATM LVAFAPPGAT IPLKPTRQML SNFYMAEVPV SAATSTMVSF S IPYTSPLS AIPTSYFGWE DWSGTNFGQL SSGSWGNLML IPSLSVDSAI PFDFQLSCWV AFGNFKAWVP RPPPPLPPLP TP AANAERT VAVIKQ UniProtKB: Genome polyprotein |
-Macromolecule #2: VP0
Macromolecule | Name: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus |
Molecular weight | Theoretical: 38.950758 KDa |
Recombinant expression | Organism: Chlorocebus sabaeus (green monkey) |
Sequence | String: GNSVTNIYGN GNNVTTDVGA NGWAPTVSTG LGDGPVSASA DSLPGRSGGA SSEKTHTVSG SSNKVGSRFS KWWEPAAARA SESATDSAI EGIDAAGKAA SKAITRKLDR PAAPSSTANP QPSLIALNPS ATQSGNASIL TGSTAPSLLA YPTATPVPLP N PDEPSQPG ...String: GNSVTNIYGN GNNVTTDVGA NGWAPTVSTG LGDGPVSASA DSLPGRSGGA SSEKTHTVSG SSNKVGSRFS KWWEPAAARA SESATDSAI EGIDAAGKAA SKAITRKLDR PAAPSSTANP QPSLIALNPS ATQSGNASIL TGSTAPSLLA YPTATPVPLP N PDEPSQPG PSGDRTWLLD TVTWSQEFTR GWNIAGSNGM QWTGLESLIF PVSTDTNWTS TSSPTAYPLP FSFVRAYPDS SW AAMYNTH SMWNCGWRVQ VTVNGSQFHA GALILYMVPE ATTHAIQTAR DNAGFVFPYV ILNLYESNTA TIEVPYISPT PNT SSGLHA PWTFYLQVLS PLNPPPSLPT SLSCSIYVTP VDSSFHGLRY LAPQ UniProtKB: Genome polyprotein |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Details: VP3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus |
Molecular weight | Theoretical: 24.082244 KDa |
Sequence | String: HWKTRAVPGA GTFGSAVAGQ ELPLCGVRAY YPPNAYIPAQ VRDWLEFAHR PGLMATVPWT MADEPAERLG IFPVSPSAIA GTGAPISYV ISLFSQWRGE LAAHLLFTGS AQHYGRLVVC YTPAAPQPPS TMQEAMRGTY TVWDVNAAST LEFTIPFISN S YWKTVDVN ...String: HWKTRAVPGA GTFGSAVAGQ ELPLCGVRAY YPPNAYIPAQ VRDWLEFAHR PGLMATVPWT MADEPAERLG IFPVSPSAIA GTGAPISYV ISLFSQWRGE LAAHLLFTGS AQHYGRLVVC YTPAAPQPPS TMQEAMRGTY TVWDVNAAST LEFTIPFISN S YWKTVDVN NPDALLSTTG YVSIWVQNPL VGPHTAPASA LVQAFISAGE SFNVRLMQNP ALTSQ UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |