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- PDB-7wva: Crystal structure of mouse Cryptochrome 1 in complex with TH401 c... -

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Basic information

Entry
Database: PDB / ID: 7wva
TitleCrystal structure of mouse Cryptochrome 1 in complex with TH401 compound
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / circadian / clock / cryptochrome / CRY / CRY1
Function / homology
Function and homology information


negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding ...negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of circadian rhythm / lipid storage / regulation of DNA damage checkpoint / response to glucagon / negative regulation of G protein-coupled receptor signaling pathway / regulation of gluconeogenesis / entrainment of circadian clock by photoperiod / E-box binding / response to light stimulus / photoreceptor activity / signal transduction in response to DNA damage / negative regulation of gluconeogenesis / phosphatase binding / positive regulation of protein ubiquitination / negative regulation of protein ubiquitination / positive regulation of gluconeogenesis / nuclear receptor binding / response to activity / gluconeogenesis / circadian regulation of gene expression / regulation of circadian rhythm / response to insulin / circadian rhythm / kinase binding / histone deacetylase binding / glucose homeostasis / double-stranded DNA binding / DNA-binding transcription factor binding / nucleotide binding / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6I3 / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMiller, S.A. / Hirota, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02402 Japan
Japan Society for the Promotion of Science (JSPS)21H04766 Japan
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
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7862
Polymers57,3721
Non-polymers4141
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein is monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20220 Å2
Unit cell
Length a, b, c (Å)44.916, 78.195, 132.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cryptochrome-1


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
#2: Chemical ChemComp-6I3 / 2-(1-methylbenzimidazol-2-yl)sulfanyl-N-[(E)-(2,3,4-trimethoxyphenyl)methylideneamino]ethanamide


Mass: 414.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0257refinement
xia2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX4

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
RfactorNum. reflection% reflection
Rfree0.2204 1456 4.84 %
Rwork0.1897 28612 -
obs0.1911 30068 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.06 Å2
Refinement stepCycle: LAST / Resolution: 2.05→67.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 29 171 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723777
X-RAY DIFFRACTIONf_angle_d0.77875169
X-RAY DIFFRACTIONf_chiral_restr0.0481564
X-RAY DIFFRACTIONf_plane_restr0.0077665
X-RAY DIFFRACTIONf_dihedral_angle_d19.59931282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.29311500.23342752X-RAY DIFFRACTION98.94
2.12-2.210.25951490.20942797X-RAY DIFFRACTION99.66
2.21-2.310.26011540.21382804X-RAY DIFFRACTION99.7
2.31-2.430.23681510.19252841X-RAY DIFFRACTION99.93
2.43-2.580.26211590.1862802X-RAY DIFFRACTION99.93
2.58-2.780.24491440.19512854X-RAY DIFFRACTION99.9
2.78-3.060.2431210.20462883X-RAY DIFFRACTION99.97
3.06-3.510.23171470.1892892X-RAY DIFFRACTION100
3.51-4.420.17191400.16332906X-RAY DIFFRACTION100
4.42-67.380.19411410.19153081X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5877959206-0.32619479672-0.05363963300452.08247149928-0.1236013145182.55708043629-0.0335102352149-0.2328152654160.0005120208955780.2063560794070.0957382644173-0.01674067173690.0950120966017-0.353482431993-0.05797457479080.199658231638-0.0116141480623-0.02375829985120.251974888014-0.0230280651820.204351715357-4.956864133476.06159947491-11.5261350106
20.6611692359950.2521438160660.06408010546512.63632158699-0.2253335174951.521369489910.0725424584788-0.1048741089480.2054120003120.0975411030114-0.06859914940520.104939606512-0.414720151112-0.0009009295574680.058749410470.281165929063-0.00325314173280.01237845605340.194641966452-0.04501044251550.3064568289465.1695949252423.5039472557-21.1174728065
32.18953101578-0.515620974317-0.1856152594741.4368536082-0.1309900901121.099272448870.2272389421210.392345721520.00617446601333-0.254928732649-0.1784359239640.0173783760543-0.153301171193-0.24429084434-0.05841355172670.2581592520940.0909536593346-0.01046594245840.266126103553-0.03071124420530.22195803179-7.6145897099315.7523006859-41.1696272408
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 229 )2 - 2291 - 223
22chain 'A' and (resid 230 through 283 )230 - 283224 - 275
33chain 'A' and (resid 284 through 494 )284 - 494276 - 480

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