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Open data
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Basic information
Entry | Database: PDB / ID: 5mjv | |||||||||||||||||||||||||||
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Title | Rebuild and re-refined model for Human Parechovirus 1 | |||||||||||||||||||||||||||
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![]() | VIRUS / PARECHOVIRUS / PICORNAVIRUS / RNA / HUMAN PARECHOVIRUS 1 / HPeV1 / HPEV | |||||||||||||||||||||||||||
Function / homology | ![]() 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 ...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 | ![]() Echovirus 22 | |||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||||||||
![]() | Shakeel, S. / Dykeman, E.C. / White, S.J. / Ora, A. / Cockburn, J.J.B. / Butcher, S.J. / Stockley, P.G. / Twarock, R. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.3 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.8 KB | Display | ![]() |
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Full document | ![]() | 486.2 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bevS S: Starting model for refinement |
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Similar structure data |
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Links
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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)) |
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Components
#1: Protein | Mass: 26417.701 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() 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.) ![]() ![]() 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.) ![]() ![]() 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.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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