+Open data
-Basic information
Entry | Database: PDB / ID: 5ktz | ||||||
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Title | expanded poliovirus in complex with VHH 12B | ||||||
Components |
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Keywords | VIRUS/immune system / poliovirus / VHH / nanobody / 80S / expanded / single domain antibody / 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / 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 | ||||||
Biological species | Poliovirus type 1 Camelus dromedarius (Arabian camel) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Strauss, M. / Schotte, L. / Filman, D.J. / Hogle, J.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Virol / Year: 2017 Title: Cryo-electron Microscopy Structures of Expanded Poliovirus with VHHs Sample the Conformational Repertoire of the Expanded State. Authors: Mike Strauss / Lise Schotte / Krishanthi S Karunatilaka / David J Filman / James M Hogle / Abstract: By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs ...By using cryo-electron microscopy, expanded 80S-like poliovirus virions (poliovirions) were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies). In all four complexes, the VHHs bind to a site on the top surface of the capsid protein VP3, which is hidden in the native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the Nanobodies has sampled a range of low-energy structures available to the expanded virion. By stabilizing unique structures of expanded virions, VHH binding permitted a more detailed view of the virus structure than was previously possible, leading to a better understanding of the expansion process that is a critical step in infection. It is now clear which polypeptide chains become disordered and which become rearranged. The higher resolution of these structures also revealed well-ordered conformations for the EF loop of VP2, the GH loop of VP3, and the N-terminal extensions of VP1 and VP2, which, in retrospect, were present in lower-resolution structures but not recognized. These structural observations help to explain preexisting mutational data and provide insights into several other stages of the poliovirus life cycle, including the mechanism of receptor-triggered virus expansion. IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The ...IMPORTANCE: When poliovirus infects a cell, it undergoes a change in its structure in order to pass RNA through its protein coat, but this altered state is short-lived and thus poorly understood. The structures of poliovirus bound to single-domain antibodies presented here capture the altered virus in what appear to be intermediate states. A careful analysis of these structures lets us better understand the molecular mechanism of infection and how these changes in the virus lead to productive-infection events. | ||||||
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 | 5ktz.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ktz.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ktz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ktz_validation.pdf.gz | 809.1 KB | Display | wwPDB validaton report |
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Full document | 5ktz_full_validation.pdf.gz | 833.8 KB | Display | |
Data in XML | 5ktz_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 5ktz_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/5ktz ftp://data.pdbj.org/pub/pdb/validation_reports/kt/5ktz | HTTPS FTP |
-Related structure data
Related structure data | 8284MC 8277C 8285C 8286C 8292C 5ku0C 5ku2C 5kwlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
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-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 25291.594 Da / Num. of mol.: 1 / Fragment: UNP residues 636-858 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300 |
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#2: Protein | Mass: 29677.301 Da / Num. of mol.: 1 / Fragment: UNP residues 70-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poliovirus type 1 (strain Mahoney) / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300 |
#3: Protein | Mass: 25777.613 Da / Num. of mol.: 1 / Fragment: UNP residues 342-572 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Poliovirus type 1 / Strain: Mahoney / Production host: Homo sapiens (human) / References: UniProt: P03300 |
#4: Antibody | Mass: 13072.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli K-12 (bacteria) |
-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 | Name: expanded poliovirus in complex with VHH 12B / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 9 MDa / Experimental value: NO |
Source (natural) | Organism: Poliovirus type 1 (strain Mahoney) |
Buffer solution | pH: 7 |
Specimen | Conc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0151 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17627 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with ...Details: Fitting protocol: rigid body restraint of structurally conserved areas, and stereochemically restrained, icosahedrally restrained flexible fitting of areas that would otherwise disagree with the map. Refinement space: reciprocal, using both Fourier amplitudes and phases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 4.3→98.6 Å / Cor.coef. Fo:Fc: 0.733 / SU B: 38.562 / SU ML: 0.589 / ESU R: 1.228 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.691 Å2
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Refine LS restraints |
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