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- PDB-7dod: Capsid structure of human sapovirus -

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Basic information

Entry
Database: PDB / ID: 7dod
TitleCapsid structure of human sapovirus
ComponentsCalicivirin
KeywordsVIRUS / CAPSID / SAPOVIRUS / CALICIVIRUS / CRYOEM / VIRUS LIKE PARTICLE
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
Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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 ...Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Caliciviridae (CV) 3C-like protein profile. / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMiyazaki, N. / Murakami, K. / Oka, T. / Iwasaki, K. / Katayama, K. / Murata, K.
Funding support Japan, 2items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
C: Calicivirin
A: Calicivirin
B: Calicivirin


Theoretical massNumber of molelcules
Total (without water)182,2613
Polymers182,2613
Non-polymers00
Water00
1
C: Calicivirin
A: Calicivirin
B: Calicivirin
x 60


Theoretical massNumber of molelcules
Total (without water)10,935,656180
Polymers10,935,656180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calicivirin
A: Calicivirin
B: Calicivirin
x 5


  • icosahedral pentamer
  • 911 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)911,30515
Polymers911,30515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Calicivirin
A: Calicivirin
B: Calicivirin
x 6


  • icosahedral 23 hexamer
  • 1.09 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,093,56618
Polymers1,093,56618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Calicivirin


Mass: 60753.645 Da / Num. of mol.: 3 / Fragment: VP1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A2Z6DUV0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23434 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00816366
ELECTRON MICROSCOPYf_angle_d0.98222369
ELECTRON MICROSCOPYf_dihedral_angle_d5.1639622
ELECTRON MICROSCOPYf_chiral_restr0.0592443
ELECTRON MICROSCOPYf_plane_restr0.0092992

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