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Yorodumi- PDB-6t40: Bovine enterovirus F3 in complex with a Cysteinylglycine dipeptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t40 | ||||||||||||
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Title | Bovine enterovirus F3 in complex with a Cysteinylglycine dipeptide | ||||||||||||
Components |
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Keywords | VIRUS / enterovirus F3 / enterovirus capsid assembly / glutathione / Cys-Gly dipeptide | ||||||||||||
Function / homology | Function and homology information : / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...: / 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 / 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 / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Enterovirus F | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||||||||
Authors | Duyvesteyn, H.M.E. / Ren, J. / Walter, T.S. / Fry, E.E. / Stuart, D.I. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Commun Biol / Year: 2020 Title: Glutathione facilitates enterovirus assembly by binding at a druggable pocket. Authors: Duyvesteyn, H.M.E. / Ren, J. / Walter, T.S. / Fry, E.E. / Stuart, D.I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t40.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t40.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 6t40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/6t40 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/6t40 | HTTPS FTP |
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-Related structure data
Related structure data | 6t48C 6t4cC 5osnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 4 types, 4 molecules ABCD
#1: Protein | Mass: 30247.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F / References: UniProt: Q2LKZ0 |
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#2: Protein | Mass: 26757.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F / References: UniProt: Q2LKZ0 |
#3: Protein | Mass: 27149.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F / References: UniProt: Q2LKZ0 |
#4: Protein | Mass: 7705.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterovirus F / References: UniProt: Q2LKZ0 |
-Non-polymers , 8 types, 759 molecules
#5: Chemical | ChemComp-GLY / | ||||||||||
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#6: Chemical | ChemComp-STE / | ||||||||||
#7: Chemical | ChemComp-K / #8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Chemical | ChemComp-CYS / | #11: Chemical | #12: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-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, sitting drop / Details: 1.5 M Ammonium Sulfate, 0.1 M Tris at pH 8.5 / PH range: 8.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→19.92 Å / Num. obs: 2361113 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.089 / Rrim(I) all: 0.234 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 5.2 % / Num. unique obs: 112481 / CC1/2: 0.4 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OSN Resolution: 1.67→19.92 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 27373509.9 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED.
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Solvent computation | Bsol: 60.4101 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.4 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 1.67→19.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.67→1.77 Å / Rfactor Rfree error: 0.002 / Total num. of bins used: 6
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