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- EMDB-4112: Aichi virus 1: empty particle -

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Basic information

Entry
Database: EMDB / ID: EMD-4112
TitleAichi virus 1: empty particle
Map dataArchie Virus 1: Empty particle
SampleAichi != Aichi virus 1

Aichi

  • Virus: Aichi virus 1
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3
Function / homology
Function and homology information


positive stranded viral RNA replication / RNA-protein covalent cross-linking / 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 / viral capsid / : / protein complex oligomerization ...positive stranded viral RNA replication / RNA-protein covalent cross-linking / 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 / viral capsid / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / RNA helicase / symbiont entry into host cell / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / 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
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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesAichi virus / AiV (virus) / Aichi virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSabin C / Fuzik T / Skubnik K / Palkova L / Lindberg AM / Plevka P
CitationJournal: 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
DepositionSep 15, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseDec 14, 2016-
UpdateApr 24, 2019-
Current statusApr 24, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lvc
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lvc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4112.png

Downloads & links

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Map

FileDownload / File: emd_4112.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArchie Virus 1: Empty particle
Voxel sizeX=Y=Z: 1.73 Å
Density
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.16843754 - 0.31216303
Average (Standard dev.)0.0019525232 (±0.015923202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-162-162-162
Dimensions324324324
Spacing324324324
CellA=B=C: 560.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.731.731.73
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z560.520560.520560.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-162-162-162
NC/NR/NS324324324
D min/max/mean-0.1680.3120.002

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Supplemental data

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Sample components

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Entire : Aichi

EntireName: Aichi
Components
  • Virus: Aichi virus 1
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3

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Supramolecule #1: Aichi virus 1

SupramoleculeName: 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
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aichi virus
Molecular weightTheoretical: 27.194688 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: 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

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Macromolecule #2: VP0

MacromoleculeName: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aichi virus
Molecular weightTheoretical: 38.950758 KDa
Recombinant expressionOrganism: Chlorocebus sabaeus (green monkey)
SequenceString: 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

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Details: VP3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: AiV (virus)
Molecular weightTheoretical: 24.082244 KDa
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 ALTSQ

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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

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5aoo

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11606
FSC plot (resolution estimation)

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