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Yorodumi- PDB-7wva: Crystal structure of mouse Cryptochrome 1 in complex with TH401 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wva | |||||||||
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Title | Crystal structure of mouse Cryptochrome 1 in complex with TH401 compound | |||||||||
Components | Cryptochrome-1 | |||||||||
Keywords | CIRCADIAN CLOCK PROTEIN / circadian / clock / cryptochrome / CRY / CRY1 | |||||||||
Function / homology | Function and homology information negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / E-box binding / entrainment of circadian clock by photoperiod ...negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / negative regulation of G protein-coupled receptor signaling pathway / lipid storage / regulation of DNA damage checkpoint / response to glucagon / regulation of gluconeogenesis / E-box binding / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / signal transduction in response to DNA damage / negative regulation of gluconeogenesis / positive regulation of gluconeogenesis / negative regulation of protein ubiquitination / FAD binding / response to activity / positive regulation of protein ubiquitination / gluconeogenesis / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / histone deacetylase binding / circadian rhythm / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Miller, S.A. / Hirota, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: F1000Res / Year: 2022 Title: A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins. Authors: Yagi, M. / Miller, S. / Nagai, Y. / Inuki, S. / Sato, A. / Hirota, T. #1: Journal: F1000Res / Year: 2022 Title: A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins Authors: Moeri, Y. / Miller, S. / Nagai, Y. / Inuk, S. / Sato, A. / Hirota, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wva.cif.gz | 240.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wva.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wva_validation.pdf.gz | 768.1 KB | Display | wwPDB validaton report |
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Full document | 7wva_full_validation.pdf.gz | 768.3 KB | Display | |
Data in XML | 7wva_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 7wva_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/7wva ftp://data.pdbj.org/pub/pdb/validation_reports/wv/7wva | HTTPS FTP |
-Related structure data
Related structure data | 6kx4S S: Starting model for refinement |
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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: 57371.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784 |
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#2: Chemical | ChemComp-6I3 / |
#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 | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.25 M NH4Cl, 22% w/v PEG 3350, 3% v/v Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→78.18 Å / Num. obs: 30136 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3 / Num. unique obs: 4271 / CC1/2: 0.891 / Rpim(I) all: 0.187 / Rrim(I) all: 0.512 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KX4 Resolution: 2.05→67.38 Å / SU ML: 0.2457 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2044 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: 37.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→67.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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