+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9517 | |||||||||
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Title | cryo-EM structure of human Aichi virus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Picornavirus / entry / receptor binding / gastroenteritis / VIRUS | |||||||||
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 (strain Human/A846/88/1989) / Aichi virus A846/88 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zhu L / Wang XX / Ren JS / Tuthill TJ / Fry EE / Rao ZH / Stuart DI | |||||||||
Funding support | China, United Kingdom, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9517.map.gz | 167.1 MB | EMDB map data format | |
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Header (meta data) | emd-9517-v30.xml emd-9517.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_9517.png | 123.5 KB | ||
Filedesc metadata | emd-9517.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9517 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9517 | HTTPS FTP |
-Validation report
Summary document | emd_9517_validation.pdf.gz | 658.9 KB | Display | EMDB validaton report |
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Full document | emd_9517_full_validation.pdf.gz | 658.5 KB | Display | |
Data in XML | emd_9517_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_9517_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9517 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9517 | HTTPS FTP |
-Related structure data
Related structure data | 5gkaMC 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_9517.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.35 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 virus A846/88
Entire | Name: Aichi virus A846/88 |
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Components |
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-Supramolecule #1: Aichi virus A846/88
Supramolecule | Name: Aichi virus A846/88 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 650132 / Sci species name: Aichi virus A846/88 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Aichi virus A846/88 |
Molecular weight | Theoretical: 6 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 300.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: capsid protein VP1
Macromolecule | Name: capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus (strain Human/A846/88/1989) |
Molecular weight | Theoretical: 27.195672 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: TLTEDLDAPQ DTGNIENGAA DNSPQPRTTF DYTGNPLPPD TKLENFFSFY RLLPMGGSGA PSLSFPADEG TIIPLDPINW LKGADVSGI AAMLSCFTYI AADLRITLRF SNPNDNPATM LVAFAPPGAT IPLKPTRQML SNFYMAEVPV SAATSTMVSF S IPYTSPLS ...String: TLTEDLDAPQ DTGNIENGAA DNSPQPRTTF DYTGNPLPPD TKLENFFSFY RLLPMGGSGA PSLSFPADEG TIIPLDPINW LKGADVSGI AAMLSCFTYI AADLRITLRF SNPNDNPATM LVAFAPPGAT IPLKPTRQML SNFYMAEVPV SAATSTMVSF S IPYTSPLS AIPTSYFGWE DWSGTNFGQL SSGSWGNLML IPSLSVDSAI PFDFQLSCWV AFGNFKAWVP RPPPPLPPLP TP AANAERT VAVIKQ |
-Macromolecule #2: capsid protein VP0
Macromolecule | Name: capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus (strain Human/A846/88/1989) |
Molecular weight | Theoretical: 38.978031 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: TNIYGNGNNV NTDVGANGWA PTVSTGLGDG PVSCTPPTPS PGDTEVPPPR KPFTFPAPPT KSGSRFSKWW EPAAARASES ATDSAIEGI DAAGKAASKA ITRKLDRPAA PSSTANPQPS LIALNPSATQ SGNASILTGS TAPSLLAYPT ATPVPLPNPD E PSQPGPSG ...String: TNIYGNGNNV NTDVGANGWA PTVSTGLGDG PVSCTPPTPS PGDTEVPPPR KPFTFPAPPT KSGSRFSKWW EPAAARASES ATDSAIEGI DAAGKAASKA ITRKLDRPAA PSSTANPQPS LIALNPSATQ SGNASILTGS TAPSLLAYPT ATPVPLPNPD E PSQPGPSG DRTWLLDTVT WSQEFTRGWN IAGSNGMQWT GLESLIFPVS TDTNWTSTSS PTAYPLPFSF VRAYPDSSWA AM YNTHSMW NCGWRVQVTV NGSQFHAGAL ILYMVPEATT HAIQTARDNA GFVFPYVILN LYESNTATIE VPYISPTPNT SSG LHAPWT FYLQVLSPLN PPPSLPTSLS CSIYVTPVDS SFHGLRYLAP Q |
-Macromolecule #3: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Aichi virus (strain Human/A846/88/1989) |
Molecular weight | Theoretical: 23.954115 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
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 ALTS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 / Details: 1*PBS, pH 7.0 |
Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III / Details: Blot for 3 seconds before plunging. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 3-22 / Number grids imaged: 1 / Number real images: 776 / Average exposure time: 2.0 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 37027 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Cooling holder cryogen: HELIUM |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: Details: filtered to 60 Ang |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 18566 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficent |
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Output model | PDB-5gka: |