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Yorodumi- PDB-8pab: Structures of the ectodomains of Atypical porcine pestivirus solv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pab | |||||||||
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Title | Structures of the ectodomains of Atypical porcine pestivirus solved by long wavelength sulphur SAD | |||||||||
Components | Genome polyprotein | |||||||||
Keywords | VIRAL PROTEIN / pestivirus / membrane protein / glycoprotein | |||||||||
Function / homology | Function and homology information ribonuclease T2 activity / host cell membrane / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm ...ribonuclease T2 activity / host cell membrane / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / proteolysis / RNA binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Atypical porcine pestivirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Aitkenhead, H. / Stuart, D.I. / El Omari, K. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Structure / Year: 2024 Title: Structural comparison of typical and atypical E2 pestivirus glycoproteins. Authors: Aitkenhead, H. / Riedel, C. / Cowieson, N. / Rumenapf, H.T. / Stuart, D.I. / El Omari, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pab.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pab.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/8pab ftp://data.pdbj.org/pub/pdb/validation_reports/pa/8pab | HTTPS FTP |
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-Related structure data
Related structure data | 8paeC 8pagC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28424.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Atypical porcine pestivirus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A1B1M0D5 | ||||
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#2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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 / pH: 5.5 Details: 0.1M Bis Tris pH 5.5, 0.2 M ammonium sulphate, 25% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 70 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.7552 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.66 Å / Num. obs: 15203 / % possible obs: 99.27 % / Redundancy: 16.9 % / Biso Wilson estimate: 29.74 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06311 / Rpim(I) all: 0.01346 / Rrim(I) all: 0.0646 / Net I/σ(I): 26.38 |
Reflection shell | Resolution: 1.8→1.865 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5021 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 1454 / CC1/2: 0.864 / Rpim(I) all: 0.1972 / Rrim(I) all: 0.5424 / % possible all: 92.92 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→50.66 Å / SU ML: 0.2257 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.4961 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50.66 Å
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Refine LS restraints |
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LS refinement shell |
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