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- EMDB-30793: Capsid structure of human sapovirus -

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Basic information

Entry
Database: EMDB / ID: EMD-30793
TitleCapsid structure of human sapovirus
Map data
Sample
  • Virus: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
    • Protein or peptide: Calicivirin
Function / homology
Function and homology information


RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat 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 ...Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat 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 / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMiyazaki N / Murakami K / Oka T / Iwasaki K / Katayama K / Murata K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)20fk0108121h0402 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H00786 Japan
CitationJournal: To Be Published
Title: Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy
Authors: Miyazaki N / Murakami K / Oka T / Iwasaki K / Katayama K / Murata K
History
DepositionDec 14, 2020-
Header (metadata) releaseDec 15, 2021-
Map releaseDec 15, 2021-
UpdateDec 15, 2021-
Current statusDec 15, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dod
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dod
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30793.png

Downloads & links

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Map

FileDownload / File: emd_30793.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.87 Å
Density
Contour LevelBy AUTHOR: 2.2 / Movie #1: 2.2
Minimum - Maximum-10.705406 - 18.068148
Average (Standard dev.)4.400669e-09 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-280-280-280
Dimensions560560560
Spacing560560560
CellA=B=C: 487.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z487.200487.200487.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-280-280-280
NC/NR/NS560560560
D min/max/mean-10.70518.0680.000

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Supplemental data

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Sample components

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Entire : Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN

EntireName: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Components
  • Virus: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
    • Protein or peptide: Calicivirin

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Supramolecule #1: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN

SupramoleculeName: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2169442
Sci species name: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Baculovirus expression vector pFastBac1-HM

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Macromolecule #1: Calicivirin

MacromoleculeName: Calicivirin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Molecular weightTheoretical: 60.753645 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MEGNGSQLGS RQHQESQAAV DPPGATGPTT SHVVVSNPEQ PNGPAQRLEM AVATGAIQSN VPEAIRNCFA VYRTFAWNDR MPAGTFLGS VSLHPNINPY TSHLSGMWAG WGGSFESRVS ISGSGVFAGR VVASVIPPGV DPSSIRDPGV LPHAFVDARI T EPVSFMIP ...String:
MEGNGSQLGS RQHQESQAAV DPPGATGPTT SHVVVSNPEQ PNGPAQRLEM AVATGAIQSN VPEAIRNCFA VYRTFAWNDR MPAGTFLGS VSLHPNINPY TSHLSGMWAG WGGSFESRVS ISGSGVFAGR VVASVIPPGV DPSSIRDPGV LPHAFVDARI T EPVSFMIP DVRNTDYHRM DGNEPTCSLG LWVYQPLINP FSTSAVSTCW VSIETKPGGD FDFCLLKPPG QRMENGVSPE GL LPRRLGY ARGNRVGGLV VGLVLVADHH QVNRHFNANS ITYGWSTAPV NPMAAEIVVK HDYTNNRNAW LSIGAKNKGP LFP GLPNHF PDSCASTLVG AMDTGRHMPA TGVCGPAIGF QDNGDVFENE TPAVMFATFN PLTGGDNTNP IALYDSINPA SLAV MCTKS NSNFDSSGFA NDKNVVVQMS WEMYTNSQQI QGRVTPMQGT NFVFTSSGAN TLALWEERLL SYDGHQAILY SSQME RTSE YFQNDNVNIP PGSMAVFNVE TNSASFQIGI REDGYMVTGG TIGTHVVLDP ETRFQYVGLL PLTAALAGPN GNSGRA RRV FQ

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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

BufferpH: 7.4
GridModel: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 23434
FSC plot (resolution estimation)

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