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- PDB-7yc2: Crystal structure of auxiliary protein in complex with human protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yc2 | ||||||
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Title | Crystal structure of auxiliary protein in complex with human protein | ||||||
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![]() | VIRAL PROTEIN / auxiliary protein | ||||||
Function / homology | ![]() Cul2-RING ubiquitin ligase complex / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gao, X. / Cui, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: SARS-CoV-2 ORF10 hijacking ubiquitination machinery reveals potential unique drug targeting sites Authors: Zhu, K. / Song, L. / Wang, L. / Hua, L. / Luo, Z. / Wang, T. / Qin, B. / Yuan, S. / Gao, X. / Mi, W. / Cui, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.8 KB | Display | ![]() |
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PDB format | ![]() | 160.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 498.6 KB | Display | ![]() |
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Full document | ![]() | 537.1 KB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ep0S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27554.486 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 782.884 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.36 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→39.65 Å / Num. obs: 19906 / % possible obs: 98.4 % / Redundancy: 3.36 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 4.13 |
Reflection shell | Resolution: 2.89→3.07 Å / Num. unique obs: 6197 / CC1/2: 0.12 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EP0 Resolution: 2.9→17.05 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.4 / Stereochemistry target values: ML
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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 max: 112.62 Å2 / Biso mean: 68.3244 Å2 / Biso min: 38.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→17.05 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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