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

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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 / Virus
Function / homologyPoliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein ...Poliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein / Picornavirus 2B protein / 3C cysteine protease (picornain 3C) / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3, picornavirus core protein 2A / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / viral capsid / virion assembly / RNA-directed RNA polymerase / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceHuman poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 11 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2004 / Release: Aug 2, 2005
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2005Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id
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
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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
Polyers80,5497
Non-polymers00
Water0
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
Polyers4,832,957420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers402,74635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers483,29642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

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

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


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


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


Mass: 20488.623 Da / Num. of mol.: 1 / Fragment: residues 390-571 / Source: (natural) Human poliovirus 1 / Details: Virus was propogated in HELA cell suspension / 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: (natural) Human poliovirus 1 / Details: Virus was propogated in HELA cell suspension / 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: (natural) Human poliovirus 1 / Details: Virus was propogated in HELA cell suspension / 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: (natural) Human poliovirus 1 / Details: Virus was propogated in HELA cell suspension / 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: (natural) Human poliovirus 1 / Details: Virus was propogated in HELA cell suspension / 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 / 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 virusVirus host category: VERTEBRATES / Virus type: VIRION
Natural hostOrganism: Homo sapiens / Strain: HELA
Buffer solutionName: 20mM HEPES, 2mM CaCl2 / Details: 20mM HEPES, 2mM CaCl2 / pH: 7.4
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
MicroscopyMicroscope model: 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 FIELDBright-field microscopy / Nominal magnification: 50000 / Calibrated magnification: 50000 / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2 mm
Specimen holderTemperature: 77 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
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
3D reconstructionMethod: icosahedrally symmetric model-based orientation search (PFT and EM3DR)
Resolution: 11 Å / Number of particles: 3641 / Nominal pixel size: 2.69 / Actual pixel size: 2.69
Magnification calibration: radial scaling to previous low-resolution reconstruction which had been calibrated to crystal structure of native virus
Symmetry type: POINT
Atomic model buildingDetails: 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)
Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL
Target criteria: amplitude-weighted phase error, and the summation of the squared model-based amplitudes.
Atomic model buildingPDB-ID: 1HXS
Number of atoms included #LASTProtein: 724 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 724

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