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- PDB-1xyr: Poliovirus 135S cell entry intermediate -

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Basic information

Entry
Database: PDB / ID: 1xyr
TitlePoliovirus 135S cell entry intermediate
Components(Genome polyprotein, Coat protein ...) x 7
KeywordsVIRUS / BETA BARREL / VIRAL CAPSID / CELL ENTRY INTERMEDIATE / Icosahedral virus
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 RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation 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 / 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) / Peptidase C3A/C3B, picornaviral ...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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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: 11 Å
AuthorsBubeck, D. / Filman, D.J. / Cheng, N. / Steven, A.C. / Hogle, J.M. / Belnap, D.M.
CitationJournal: J Virol / Year: 2005
Title: The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.
Authors: Doryen Bubeck / David J Filman / Naiqian Cheng / Alasdair C Steven / James M Hogle / David M Belnap /
Abstract: Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational ...Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational change to the 135S cell entry intermediate. This transition involves shifts of the capsid protein beta barrels, accompanied by the externalization of VP4 and the N terminus of VP1. Both polypeptides associate with membranes and are postulated to facilitate entry by forming a translocation pore for the viral RNA. We have calculated cryo-electron microscopic reconstructions of 135S particles that permit accurate placement of the beta barrels, loops, and terminal extensions of the capsid proteins. The reconstructions and resulting models indicate that each N terminus of VP1 exits the capsid though an opening in the interface between VP1 and VP3 at the base of the canyon that surrounds the fivefold axis. Comparison with reconstructions of 135S particles in which the first 31 residues of VP1 were proteolytically removed revealed that the externalized N terminus is located near the tips of propeller-like features surrounding the threefold axes rather than at the fivefold axes, as had been proposed in previous models. These observations have forced a reexamination of current models for the role of the 135S particle in transmembrane pore formation and suggest testable alternatives.
History
DepositionNov 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 14, 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
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
Remark 999SEQUENCE VP1: Chain 1 consists of residues 71-302 of VP1. The residues that make up Chain 8 have ...SEQUENCE VP1: Chain 1 consists of residues 71-302 of VP1. The residues that make up Chain 8 have been identified as residues 42-52 but the identification is very tentative at this point. Residues 1-41 and 53-70 of VP1 are not present in the model. The authors suspect that residues 1-41 are mostly disordered, and that residues 53-70 may be differently ordered than in the native, but are not buildable at this resolution. VP2: Chain 2 consists of residues 28-264 of VP2. Chain 7 includes residues 13-26 from a (icosahedral-symmetry-related) copy of VP2. An alpha carbon from residue 27 is deliberately missing from the rigid-body model to create a hinge point for the modeling. Residues 26 (of chain 7) and 28 (of chain 2) are very far from one another in space because they come from different icosahedral-symmetry-related copies of VP2. Residues 1-12 of VP2 are probably disordered. Residues 265-272 of VP2 could not be modeled. VP3: Alpha carbons for 13 and 49 were deliberately omitted from the rigid-body model, to create hinge points for the modeling. C-terminal residues 232-235 or 233-235 (chain 3) are missing from all of the high-resolution (type 1 mahoney) native poliovirus structures, either due to disorder or proteolysis. AUTHOR HAS MODELLED RESIDUES 123 OF CHAIN 3 AS SER, WHEREAS THE CORRESPONDING RESIDUE 463 IN SWISSPROT IS PHE. THE AUTHOR CLAIMS THERE IS AN ERROR IN SWISSPROT AND THAT RESIDUE 123 SHOULD BE SER.

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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
  • EMDB-1133
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  • Simplified surface model + fitted atomic model
  • EMDB-1136
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  • Simplified surface model + fitted atomic model
  • EMDB-1137
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  • Simplified surface model + fitted atomic model
  • EMDB-1144
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  • Simplified surface model + fitted atomic model
  • EMDB-1145
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Assembly

Deposited unit
1: Genome polyprotein, Coat protein VP1
2: Genome polyprotein, Coat protein VP2
3: Genome polyprotein, Coat protein VP3
5: Genome polyprotein, Coat protein VP3
6: Genome polyprotein, Coat protein VP3
7: Genome polyprotein, Coat protein VP2
8: Genome polyprotein, Coat protein VP1


Theoretical massNumber of molelcules
Total (without water)80,5497
Polymers80,5497
Non-polymers00
Water00
1
1: Genome polyprotein, Coat protein VP1
2: Genome polyprotein, Coat protein VP2
3: Genome polyprotein, Coat protein VP3
5: Genome polyprotein, Coat protein VP3
6: Genome polyprotein, Coat protein VP3
7: Genome polyprotein, Coat protein VP2
8: Genome polyprotein, Coat protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)4,832,957420
Polymers4,832,957420
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: Genome polyprotein, Coat protein VP1
2: Genome polyprotein, Coat protein VP2
3: Genome polyprotein, Coat protein VP3
5: Genome polyprotein, Coat protein VP3
6: Genome polyprotein, Coat protein VP3
7: Genome polyprotein, Coat protein VP2
8: Genome polyprotein, Coat protein VP1
x 5


  • icosahedral pentamer
  • 403 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)402,74635
Polymers402,74635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Genome polyprotein, Coat protein VP1
2: Genome polyprotein, Coat protein VP2
3: Genome polyprotein, Coat protein VP3
5: Genome polyprotein, Coat protein VP3
6: Genome polyprotein, Coat protein VP3
7: Genome polyprotein, Coat protein VP2
8: Genome polyprotein, Coat protein VP1
x 6


  • icosahedral 23 hexamer
  • 483 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)483,29642
Polymers483,29642
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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Genome polyprotein, Coat protein ... , 7 types, 7 molecules 1235678

#1: Protein Genome polyprotein, Coat protein VP1 / Coordinate model: Cα atoms only


Mass: 26135.506 Da / Num. of mol.: 1 / Fragment: residues 649-880 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#2: Protein Genome polyprotein, Coat protein VP2 / Coordinate model: Cα atoms only


Mass: 26244.518 Da / Num. of mol.: 1 / Fragment: residues 96-332 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#3: Protein Genome polyprotein, Coat protein VP3 / Coordinate model: Cα atoms only


Mass: 20488.623 Da / Num. of mol.: 1 / Fragment: residues 390-571 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#4: Protein/peptide Genome polyprotein, Coat protein VP3 / Coordinate model: Cα atoms only


Mass: 1214.349 Da / Num. of mol.: 1 / Fragment: residues 341-352 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#5: Protein/peptide Genome polyprotein, Coat protein VP3 / Coordinate model: Cα atoms only


Mass: 3947.482 Da / Num. of mol.: 1 / Fragment: residues 354-389 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#6: Protein/peptide Genome polyprotein, Coat protein VP2 / Coordinate model: Cα atoms only


Mass: 1488.682 Da / Num. of mol.: 1 / Fragment: residues 81-94 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / References: UniProt: P03300
#7: Protein/peptide Genome polyprotein, Coat protein VP1 / Coordinate model: Cα atoms only


Mass: 1030.129 Da / Num. of mol.: 1 / Fragment: residues 620-630 / Source method: isolated from a natural source / Details: Virus was propogated in HELA cell suspension / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Type 1 Mahoney / 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 135S CELL ENTRY INTERMEDIATE / Type: VIRUS
Details: 135S was made by heating native virus in 20mM HEPES pH 7.4, 2mM CaCl2 at 50 degrees for 3 minutes
Details of virusHost category: VERTEBRATES / Type: VIRION
Natural hostOrganism: Homo sapiens / Strain: HELA
Buffer solutionName: 20mM HEPES, 2mM CaCl2 / pH: 7.4 / Details: 20mM HEPES, 2mM CaCl2
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil Holey Carbon Grids (R2/2)
VitrificationCryogen name: ETHANE / Details: 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: Sep 17, 2002 / Details: Focal pairs were taken
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Specimen holderTemperature: 77 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 1 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1INSOUTmodel fittingrigid body
2EM3DR3D reconstruction
CTF correctionDetails: CTF correction of each particle. Phase flipped correction for particles included in the orientation search, and deconvoluted and gaussian decay corrected for the particles used in the reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: icosahedrally symmetric model-based orientation search (PFT and EM3DR)
Resolution: 11 Å / Num. of particles: 3641 / Nominal pixel size: 2.69 Å / Actual pixel size: 2.69 Å
Magnification calibration: radial scaling to previous low-resolution reconstruction which had been calibrated to crystal structure of native virus
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL
Target criteria: amplitude-weighted phase error, and the summation of the squared model-based amplitudes.
Details: METHOD--gradient search REFINEMENT PROTOCOL--Rigid body (chains 1 and 6 as one rigid body, chains 3 and 7 as one rigid body, chains 2 and 8 as individual rigid bodies, chain 5 placed along 5fold axis visually)
Atomic model buildingPDB-ID: 1HXS

1hxs


Accession code: 1HXS / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 0 0 724

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