+Open data
-Basic information
Entry | Database: PDB / ID: 5mjv | |||||||||||||||||||||||||||
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Title | Rebuild and re-refined model for Human Parechovirus 1 | |||||||||||||||||||||||||||
Components |
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Keywords | VIRUS / PARECHOVIRUS / PICORNAVIRUS / RNA / HUMAN PARECHOVIRUS 1 / HPeV1 / HPEV | |||||||||||||||||||||||||||
Function / homology | Function and homology information host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Human parechovirus 1 Echovirus 22 | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | |||||||||||||||||||||||||||
Authors | Shakeel, S. / Dykeman, E.C. / White, S.J. / Ora, A. / Cockburn, J.J.B. / Butcher, S.J. / Stockley, P.G. / Twarock, R. | |||||||||||||||||||||||||||
Funding support | Finland, United Kingdom, 8items
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Citation | Journal: Nat Commun / Year: 2017 Title: Genomic RNA folding mediates assembly of human parechovirus. Authors: Shakeel, S. / Dykeman, E.C. / White, S.J. / Ora, A. / Cockburn, J.J. / Butcher, S.J. / Stockley, P.G. / Twarock, R. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mjv.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mjv.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjv ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjv | HTTPS FTP |
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-Related structure data
Related structure data | 1bevS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 26417.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
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#2: Protein | Mass: 28293.186 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line: A549 / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#3: Protein | Mass: 31693.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase |
#4: RNA chain | Mass: 1831.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echovirus 22 (strain Harris) / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1M TRIS PH 8.0, 0.6M AMMONIUM SULFATE, 0.1M MGCL2, 5% (W/V) GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→345.977 Å / Num. obs: 233083 / % possible obs: 78.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.354 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 0.9 / % possible all: 31.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BEV Resolution: 3.09→345.977 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.09→345.977 Å
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