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- EMDB-9517: cryo-EM structure of human Aichi virus -

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Basic information

Entry
Database: EMDB / ID: EMD-9517
Titlecryo-EM structure of human Aichi virus
Map data
Sample
  • Virus: Aichi virus A846/88
    • Protein or peptide: capsid protein VP1
    • Protein or peptide: capsid protein VP0
    • Protein or peptide: Genome polyprotein
KeywordsPicornavirus / 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 ...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 / RNA-directed RNA polymerase / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus ...LRAT domain profile. / LRAT domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesAichi virus (strain Human/A846/88/1989) / Aichi virus A846/88
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhu L / Wang XX / Ren JS / Tuthill TJ / Fry EE / Rao ZH / Stuart DI
Funding support China, United Kingdom, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology2014CB542800 China
Medical Research Council (United Kingdom)G100099 United Kingdom
CitationJournal: 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
DepositionJul 4, 2016-
Header (metadata) releaseAug 3, 2016-
Map releaseSep 21, 2016-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gka
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5gka
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9517.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.21457675 - 0.3053629
Average (Standard dev.)0.0015915065 (±0.015703281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.2150.3050.002

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Supplemental data

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Sample components

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Entire : Aichi virus A846/88

EntireName: Aichi virus A846/88
Components
  • Virus: Aichi virus A846/88
    • Protein or peptide: capsid protein VP1
    • Protein or peptide: capsid protein VP0
    • Protein or peptide: Genome polyprotein

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Supramolecule #1: Aichi virus A846/88

SupramoleculeName: 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
Host (natural)Organism: Aichi virus A846/88
Molecular weightTheoretical: 6 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Macromolecule #1: capsid protein VP1

MacromoleculeName: capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aichi virus (strain Human/A846/88/1989)
Molecular weightTheoretical: 27.195672 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: 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

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Macromolecule #2: capsid protein VP0

MacromoleculeName: capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aichi virus (strain Human/A846/88/1989)
Molecular weightTheoretical: 38.978031 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: 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

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aichi virus (strain Human/A846/88/1989)
Molecular weightTheoretical: 23.954115 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7 / Details: 1*PBS, pH 7.0
GridModel: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III / Details: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37027 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: HELIUM
Image recordingFilm 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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

Details: filtered to 60 Ang
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 18566

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: correlation coefficent
Output model

PDB-5gka:
cryo-EM structure of human Aichi virus

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