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- PDB-3jbf: Complex of poliovirus with VHH PVSP19B -

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Basic information

Entry
Database: PDB / ID: 3jbf
TitleComplex of poliovirus with VHH PVSP19B
Components
  • (Capsid protein ...Capsid) x 4
  • nanobody VHH PVSP19B
KeywordsVIRUS/IMMUNE SYSTEM / poliovirus / nanobodies / VHH / neutralizing antibodies / VIRUS-IMMUNE SYSTEM complex
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 / T=pseudo3 icosahedral viral capsid / picornain 3C / 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 / virion assembly / viral capsid / 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 sourceCamelus dromedarius (Arabian camel)
Human poliovirus 1 Mahoney
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsStrauss, M. / Schotte, L. / Thys, B. / Filman, D.J. / Hogle, J.M.
CitationJournal: J. Virol. / Year: 2016
Title: Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.
Authors: Mike Strauss / Lise Schotte / Bert Thys / David J Filman / James M Hogle
Abstract: Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In ...Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion.
IMPORTANCE: We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 26, 2015 / Release: Jan 27, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 27, 2016Structure modelrepositoryInitial release
1.1Mar 30, 2016Structure modelDatabase references
1.2Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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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
  • EMDB-6434
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
7: nanobody VHH PVSP19B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9086
Polyers111,6525
Non-polymers2561
Water0
1
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
7: nanobody VHH PVSP19B
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)6,714,483360
Polyers6,699,097300
Non-polymers15,38560
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
7: nanobody VHH PVSP19B
hetero molecules
x 5


  • icosahedral pentamer
  • 560 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)559,54030
Polyers558,25825
Non-polymers1,2825
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: Capsid protein VP1
2: Capsid protein VP2
3: Capsid protein VP3
4: Capsid protein VP4
7: nanobody VHH PVSP19B
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 671 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)671,44836
Polyers669,91030
Non-polymers1,5396
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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Capsid protein ... , 4 types, 4 molecules 1234

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


Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881 / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#2: Protein/peptide Capsid protein VP2 / / P1B / Virion protein 2


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341 / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#3: Protein/peptide Capsid protein VP3 / / P1C / Virion protein 3


Mass: 26419.352 Da / Num. of mol.: 1 / Fragment: UNP residues 342-578 / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300
#4: Protein/peptide Capsid protein VP4 / / P1A / Virion protein 4


Mass: 7603.405 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300

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Protein/peptide / Non-polymers , 2 types, 2 molecules 7

#5: Protein/peptide nanobody VHH PVSP19B


Mass: 14064.470 Da / Num. of mol.: 1 / Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid details: pHEN6(c) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Formula: C16H32O2 / Palmitic acid

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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

Component
IDNameTypeDetailsParent ID
1Nanobody PVSS8A in complex with poliovirus P1/MahoneyCOMPLEX60 nanobody VHH monomers bind to each poliovirion0
2Human poliovirus 1VIRUS1
3PVSP19B1
Molecular weightValue: 9 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus isolate: SEROTYPE / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 145 mM NaCl, 50 mM Na2HPO4.12H2O / Details: 145 mM NaCl, 50 mM Na2HPO4.12H2O / pH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-flat 1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 154 K
Details: Blotted for 4 seconds before plunging into liquid ethane (homemade plunger).
Method: 4 second blot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Nov 27, 2013 / Details: Gatan K2 operated in Super-resolution mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 23000 / Calibrated magnification: 25381 / Nominal defocus max: -4000 nm / Nominal defocus min: -1400 nm / Cs: 2.26 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Polara holder / Temperature: 80 kelvins / Temperature (max): 110 kelvins / Temperature (min): 80 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNumber digital images: 300

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Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2REFMAC5model fitting
3SPDBVmodel fitting
4FREALIGN3D reconstruction
CTF correctionDetails: per particle
SymmetryPoint symmetry: I
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18009 / Nominal pixel size: 0.985 / Actual pixel size: 0.985
Details: (Single particle details: The particles were processed using Frealign.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--flexible DETAILS--Using stereochemically and icosahedrally restrained maximum likelihood refinement in REFMAC5, a representative subset of the full atomic model with all neighbors present was built and refined to fit the corresponding subset of the experimental map. Portions of the model whose density resembled a structural homolog were identified and restrained to agree with the homolog. Detailed atomic models were constructed in areas of difference wherever the resolution of the map permitted. The Fourier-amplitude-weighted average cosine of the phase discrepancy was tracked.
Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL
Target criteria: ML agreement with Fourier amplitudes and phases
Atomic model buildingPDB-ID: 1I3U
RefineCorrelation coeff Fo to Fc: 0.702 / Overall SU B: 110.77 / Overall SU ML: 1.342 / Sigma F: 0 / Overall ESU R: 1.58
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: NONE
Displacement parametersB iso max: 5 Å2 / B iso mean: 24.734 Å2 / B iso min: 1 Å2 / Aniso B11: 0.84 Å2 / Aniso B12: -0.29 Å2 / Aniso B13: -0.44 Å2 / Aniso B22: 1.05 Å2 / Aniso B23: -0.74 Å2 / Aniso B33: -1.88 Å2
Least-squares processR factor R work: 0.4648 / R factor obs: 0.4648 / Highest resolution: 4.6 Å / Lowest resolution: 95.15 Å / Number reflection obs: 207196 / Percent reflection obs: 99.99
Refine hist #LASTHighest resolution: 4.6 Å / Lowest resolution: 95.15 Å
Number of atoms included #LASTProtein: 7612 / Nucleic acid: 0 / Ligand: 18 / Solvent: 0 / Total: 7630
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0100.01944004
ELECTRON MICROSCOPYr_angle_refined_deg2.1031.95559966
ELECTRON MICROSCOPYr_dihedral_angle_1_deg0.2975.0005457
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.77423.9571893
ELECTRON MICROSCOPYr_dihedral_angle_3_deg2.35415.0006884
ELECTRON MICROSCOPYr_dihedral_angle_4_deg3.17515.000234
ELECTRON MICROSCOPYr_chiral_restr0.1670.2006694
ELECTRON MICROSCOPYr_gen_planes_refined0.0010.02133590
Refine LS shellHighest resolution: 4.6 Å / R factor R work: 0.541 / Lowest resolution: 4.848 Å / Number reflection R work: 30241 / Total number of bins used: 10 / Percent reflection obs: 1

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