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Yorodumi- PDB-7d1c: Crystal structure of mouse Cryptochrome 1 in complex with compoun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d1c | |||||||||
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Title | Crystal structure of mouse Cryptochrome 1 in complex with compound TH303 | |||||||||
Components | Cryptochrome-1 | |||||||||
Keywords | CIRCADIAN CLOCK PROTEIN / Cryptochrome / CRY / CRY1 / clock | |||||||||
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 / entrainment of circadian clock by photoperiod / E-box binding ...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 / entrainment of circadian clock by photoperiod / E-box binding / photoreceptor activity / response to light stimulus / phosphatase binding / negative regulation of gluconeogenesis / signal transduction in response to DNA damage / 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 / circadian rhythm / histone deacetylase binding / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | |||||||||
Authors | Miller, S.A. / Hirota, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock. Authors: Kolarski, D. / Miller, S. / Oshima, T. / Nagai, Y. / Aoki, Y. / Kobauri, P. / Srivastava, A. / Sugiyama, A. / Amaike, K. / Sato, A. / Tama, F. / Szymanski, W. / Feringa, B.L. / Itami, K. / Hirota, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d1c.cif.gz | 253.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d1c.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 7d1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/7d1c ftp://data.pdbj.org/pub/pdb/validation_reports/d1/7d1c | HTTPS FTP |
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-Related structure data
Related structure data | 7d19C 6kx4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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-GOF / |
#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: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.25 M NH4Cl, 23% PEG w/v 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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→67.78 Å / Num. obs: 37588 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.062 / Rrim(I) all: 0.133 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5359 / CC1/2: 0.837 / Rpim(I) all: 0.208 / Rrim(I) all: 0.453 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KX4 Resolution: 1.91→42.7 Å / SU ML: 0.1821 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.616 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: 26.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→42.7 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 |
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