+Open data
-Basic information
Entry | Database: PDB / ID: 7ye8 | ||||||
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Title | Crystal structure of SARS-CoV-2 refolded dimeric ORF9b | ||||||
Components | ORF9b protein | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / ORF9b / immune escape / viral antagonist / membrane association / fold switch / lipid binding | ||||||
Function / homology | Function and homology information Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / host cell mitochondrion / negative regulation of mitochondrial fission / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / host cell mitochondrion / negative regulation of mitochondrial fission / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial outer membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Jin, X. / Chai, Y. / Qi, J. / Song, H. / Gao, G.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci China Life Sci / Year: 2023 Title: Structural characterization of SARS-CoV-2 dimeric ORF9b reveals potential fold-switching trigger mechanism. Authors: Jin, X. / Sun, X. / Chai, Y. / Bai, Y. / Li, Y. / Hao, T. / Qi, J. / Song, H. / Wong, C.C.L. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ye8.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ye8.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ye8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ye8_validation.pdf.gz | 809.7 KB | Display | wwPDB validaton report |
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Full document | 7ye8_full_validation.pdf.gz | 812.8 KB | Display | |
Data in XML | 7ye8_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7ye8_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7ye8 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7ye8 | HTTPS FTP |
-Related structure data
Related structure data | 7ye7C 2cmeS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11637.517 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: 9b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DTD2 #2: Chemical | 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 | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8M sodium phosphate monobasic monohydrate, 0.8M potassium phosphate monobasic, 0.1M sodium HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 11680 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 41.41 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 46.615 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 19.5 % / Rmerge(I) obs: 1.392 / Mean I/σ(I) obs: 3 / Num. unique obs: 302 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CME Resolution: 3.01→28.29 Å / SU ML: 0.3415 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4451 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: 52.51 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→28.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -23.1009533282 Å / Origin y: 27.0139829072 Å / Origin z: 16.406639538 Å
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Refinement TLS group | Selection details: all |