+Open data
-Basic information
Entry | Database: PDB / ID: 3jbc | |||||||||
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Title | Complex of Poliovirus with VHH PVSP29F | |||||||||
Components |
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Keywords | VIRUS/IMMUNE SYSTEM / VHH / nanobody / poliovirus / VIRUS-IMMUNE SYSTEM complex | |||||||||
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 / 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / 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 RIG-I activity / 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 MAVS 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 / channel activity / nucleoside-triphosphate phosphatase / monoatomic ion transmembrane transport / 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 / virus-mediated perturbation of host defense response / 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 | |||||||||
Biological species | Camelus dromedarius (Arabian camel) Human poliovirus 1 Mahoney | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Strauss, M. / Schotte, L. / Thys, B. / Filman, D.J. / Hogle, J.M. | |||||||||
Citation | Journal: 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 ...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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jbc.cif.gz | 177.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jbc.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 3jbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jbc_validation.pdf.gz | 931.2 KB | Display | wwPDB validaton report |
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Full document | 3jbc_full_validation.pdf.gz | 960.6 KB | Display | |
Data in XML | 3jbc_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 3jbc_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbc ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbc | HTTPS FTP |
-Related structure data
Related structure data | 5888M 6433C 6434C 6435C 3jbdC 3jbeC 3jbfC 3jbgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Capsid protein ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 33488.613 Da / Num. of mol.: 1 / Fragment: UNP residues 580-881 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300 |
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#2: Protein | Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: UNP residues 70-341 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300 |
#3: Protein | Mass: 26419.352 Da / Num. of mol.: 1 / Fragment: UNP residues 342-578 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300 |
#4: Protein | Mass: 7603.405 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Human poliovirus 1 Mahoney / Strain: Mahoney / References: UniProt: P03300 |
-Antibody / Non-polymers , 2 types, 2 molecules 7
#5: Antibody | Mass: 14388.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid details: pHEN6(c) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 |
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#6: Chemical | ChemComp-PLM / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 9 MDa / Experimental value: NO | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Buffer solution | Name: PBS / pH: 7.4 / Details: 145 mM NaCl, 50 mM Na2HPO4.12H2O | ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 154 K / Details: Plunged into liquid ethane (homemade plunger). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Oct 23, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Calibrated magnification: 89232 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 1503 |
-Processing
EM software |
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CTF correction | Details: per particle | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9764 / Nominal pixel size: 1.681 Å / Actual pixel size: 1.681 Å Details: (Single particle details: processed with frealign) (Single particle--Applied symmetry: I) Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL Target criteria: Stereochemically restrained maximum likelihood refinement of both Fourier phase and amplitude agreement Details: REFINEMENT PROTOCOL--Rigid body with some flexible loops and side chains DETAILS--LSQKAB was applied after each refinement cycle to re-impose exact icosahedral operators and rigid body constraints. | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 5.6→97.84 Å / Cor.coef. Fo:Fc: 0.76 / SU B: 182.456 / SU ML: 1.841 / σ(F): 0 / ESU R: 15.023 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50 Å2 / Biso mean: 24.7 Å2 / Biso min: 10 Å2
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Refinement step | Cycle: LAST / Resolution: 5.6→97.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 5.601→5.903 Å / Total num. of bins used: 10
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