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- PDB-3j48: Cryo-EM structure of Poliovirus 135S particles -

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Basic information

Entry
Database: PDB / ID: 3j48
TitleCryo-EM structure of Poliovirus 135S particles
Components
  • Protein VP1
  • Protein VP2
  • Protein VP3
KeywordsVIRUS / cell entry / single particle analysis
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / 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 / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / 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 speciesHuman poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsButan, C. / Fiman, D.J. / Hogle, J.M.
CitationJournal: J Virol / Year: 2014
Title: Cryo-electron microscopy reconstruction shows poliovirus 135S particles poised for membrane interaction and RNA release.
Authors: Carmen Butan / David J Filman / James M Hogle /
Abstract: During infection, binding of mature poliovirus to cell surface receptors induces an irreversible expansion of the capsid, to form an infectious cell-entry intermediate particle that sediments at 135S. ...During infection, binding of mature poliovirus to cell surface receptors induces an irreversible expansion of the capsid, to form an infectious cell-entry intermediate particle that sediments at 135S. In these expanded virions, the major capsid proteins (VP1 to VP3) adopt an altered icosahedral arrangement to open holes in the capsid at 2-fold and quasi-3-fold axes, and internal polypeptides VP4 and the N terminus of VP1, which can bind membranes, become externalized. Cryo-electron microscopy images for 117,330 particles were collected using Leginon and reconstructed using FREALIGN. Improved rigid-body positioning of major capsid proteins established reliably which polypeptide segments become disordered or rearranged. The virus-to-135S transition includes expansion of 4%, rearrangements of the GH loops of VP3 and VP1, and disordering of C-terminal extensions of VP1 and VP2. The N terminus of VP1 rearranges to become externalized near its quasi-3-fold exit, binds to rearranged GH loops of VP3 and VP1, and attaches to the top surface of VP2. These details improve our understanding of subsequent stages of infection, including endocytosis and RNA transfer into the cytoplasm.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • 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
1: Protein VP1
2: Protein VP2
3: Protein VP3


Theoretical massNumber of molelcules
Total (without water)90,1123
Polymers90,1123
Non-polymers00
Water0
1
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,406,713180
Polymers5,406,713180
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
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,55915
Polymers450,55915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Protein VP1
2: Protein VP2
3: Protein VP3
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)540,67118
Polymers540,67118
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Protein VP1 / P1D / Virion protein 1 / Coordinate model: Cα atoms only


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: P03300
#2: Protein Protein VP2 / P1B / Virion protein 2 / Coordinate model: Cα atoms only


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: P03300
#3: Protein Protein VP3 / P1C / Virion protein 3 / Coordinate model: Cα atoms only


Mass: 26547.482 Da / Num. of mol.: 1 / Fragment: UNP residues 342-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Strain: Mahoney / Cell line (production host): HeLa / Production host: Homo sapiens (human) / References: UniProt: P03300

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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: Poliovirus 1 Mahoney 135S particle / Type: VIRUS
Details: icosahedrally ordered capsid: 60 copies of VP1, VP2, VP3
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
118.6 MDaYES
219 MDaNO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 20 mM HEPES, 2 mM CaCl2 / pH: 7.4 / Details: 20 mM HEPES, 2 mM CaCl2
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon-grids (200 mesh C-flat grids)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 90 K
Details: Blotted manually in ambient atmosphere before plunging into ethane cooled by liquid nitrogen.
Method: Blotted manually before plunge freezing into liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 28, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 62000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 980 nm / Cs: 2 mm / Astigmatism: Objective lens astigmatism was corrected
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Specimen holder type: Side entry liquid nitrogen-cooled cryo specimen holder
Temperature: 90 K / Temperature (max): 93 K / Temperature (min): 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Image scansNum. digital images: 1020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2REFMACmodel fitting
3FREALIGN3D reconstruction
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FREALIGN randomized search / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117330 / Nominal pixel size: 1.37 Å / Actual pixel size: 1.37 Å
Details: Single particle details: The particles were selected using an automatic selection program (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL
Target criteria: mean amplitude-weighted cosine of the phase difference
Details: METHOD--rigid body REFINEMENT PROTOCOL--rigid body DETAILS--Most of the model was docked, with specific areas of discrepancy fitted. The fitting was rigid body with flexible fitting or ...Details: METHOD--rigid body REFINEMENT PROTOCOL--rigid body DETAILS--Most of the model was docked, with specific areas of discrepancy fitted. The fitting was rigid body with flexible fitting or deletion of selected polypeptide segments. Rigid bodies for VP1, VP2, VP3, and the VP3 beta tube were defined to include beta barrels and non-covalently attached polypeptides. Each rigid body was repeatedly fitted manually and then refined. Disordered polypeptide segments were removed. Several rearranged segments were included as approximate backbone traces and refined.
Atomic model building

3D fitting-ID: 1 / Accession code: 1POV / Initial refinement model-ID: 1 / PDB-ID: 1POV

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
10
21
33
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 0 0 690

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