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- PDB-8ay5: Human rhinovirus 2 empty particle in situ -

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Basic information

Entry
Database: PDB / ID: 8ay5
TitleHuman rhinovirus 2 empty particle in situ
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • VP3
KeywordsVIRUS / Human rhinovirus 2 / empty particle / in situ / cryo-EM.
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / 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 / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 speciesrhinovirus A2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsIshemgulova, A. / Mukhamedova, L. / Trebichalska, Z. / Payne, P. / Smerdova, L. / Moravcova, J. / Hrebik, D. / Buchta, D. / Skubnik, K. / Fuzik, T. ...Ishemgulova, A. / Mukhamedova, L. / Trebichalska, Z. / Payne, P. / Smerdova, L. / Moravcova, J. / Hrebik, D. / Buchta, D. / Skubnik, K. / Fuzik, T. / Novacek, J. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGX19-25982X Czech Republic
CitationJournal: To Be Published
Title: Endosome rupture enables enteroviruses to infect cells.
Authors: Ishemgulova, A.
History
DepositionSep 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)82,8593
Polymers82,8593
Non-polymers00
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)4,971,520180
Polymers4,971,520180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein VP1 / / P1D / Virion protein 1


Mass: 28851.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2
Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells.
References: UniProt: P04936
#2: Protein Capsid protein VP2 / / P1B / Virion protein 2


Mass: 27899.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2
Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells.
References: UniProt: P04936
#3: Protein VP3


Mass: 26107.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) rhinovirus A2
Plasmid details: Rhinovirus 2 is initially purified and used for infection of cells. Micrographs were collected on lamellipodia of infected Cos7 cells.
References: UniProt: P04936

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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: rhinovirus A2 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: rhinovirus A2
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategoryDetails
1crYOLO1.5.4particle selectionmanual picking
4RELIONCTF correction
5Gctfv1.06CTF correction
8UCSF Chimera1.16model fitting
10RELIONinitial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 332
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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