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- PDB-8gqe: Crystal structure of the W285A mutant of UVR8 in complex with RUP2 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gqe | ||||||
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Title | Crystal structure of the W285A mutant of UVR8 in complex with RUP2 | ||||||
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![]() | SIGNALING PROTEIN | ||||||
Function / homology | ![]() chloroplast organization / flower development / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / plastid / photoreceptor activity / regulation of protein-containing complex assembly / response to UV / guanyl-nucleotide exchange factor activity ...chloroplast organization / flower development / entrainment of circadian clock / Cul4-RING E3 ubiquitin ligase complex / response to UV-B / plastid / photoreceptor activity / regulation of protein-containing complex assembly / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.D. / Wang, L.X. / Guan, Z.Y. / chang, H.F. / Yin, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: RUP2 facilitates UVR8 redimerization via two interfaces. Authors: Wang, L. / Wang, Y. / Chang, H. / Ren, H. / Wu, X. / Wen, J. / Guan, Z. / Ma, L. / Qiu, L. / Yan, J. / Zhang, D. / Huang, X. / Yin, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | 251.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4dnvS 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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Unit cell |
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Components
#1: Protein | Mass: 40236.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 47269.160 Da / Num. of mol.: 1 / Mutation: W285A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.68 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, Ammonium chloride, Hexamminecobalt (III) chloride, sucrose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 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→45 Å / Num. obs: 76777 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.957 / CC star: 0.989 / Rpim(I) all: 0.044 / Rrim(I) all: 0.166 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique obs: 7644 / CC1/2: 0.89 / CC star: 0.97 / Rpim(I) all: 0.241 / Rrim(I) all: 0.884 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DNV Resolution: 2→34.01 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.28 / 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: 124.29 Å2 / Biso mean: 40.4232 Å2 / Biso min: 18.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→34.01 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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Refinement TLS params. | Method: refined / Origin x: 41.4805 Å / Origin y: 69.8859 Å / Origin z: 62.1317 Å
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Refinement TLS group |
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