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- PDB-6lue: Crystal structure of mouse Cryptochrome 1 in complex with compoun... -

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Basic information

Entry
Database: PDB / ID: 6lue
TitleCrystal structure of mouse Cryptochrome 1 in complex with compound KL201
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / Cryptochrome / CRY / circadian clock / KL201
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
DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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. ...DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / 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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EUL / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMiller, S. / Aikawa, Y. / Hirota, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR14LA Japan
Japan Society for the Promotion of Science (JSPS)15H05590 Japan
Japan Society for the Promotion of Science (JSPS)18H02402 Japan
CitationJournal: Cell Chem Biol / Year: 2020
Title: An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals.
Authors: Miller, S. / Aikawa, Y. / Sugiyama, A. / Nagai, Y. / Hara, A. / Oshima, T. / Amaike, K. / Kay, S.A. / Itami, K. / Hirota, T.
History
DepositionJan 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cryptochrome-1
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5204
Polymers114,7432
Non-polymers7772
Water7,098394
1
A: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7602
Polymers57,3721
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cryptochrome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7602
Polymers57,3721
Non-polymers3881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.551, 143.260, 76.730
Angle α, β, γ (deg.)90.000, 118.650, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Cryptochrome-1 /


Mass: 57371.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P97784
#2: Chemical ChemComp-EUL / 2-bromanyl-N-(5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-yl)benzamide


Mass: 388.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14BrN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% w/v PEG 3350, 3% v/v ethylene glycol, 200 mM NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→41.45 Å / Num. obs: 71867 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.091 / Net I/σ(I): 6.6
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 10493 / CC1/2: 0.545 / Rpim(I) all: 0.31

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0R

4k0r


Resolution: 2.1→40.46 Å / SU ML: 0.2879 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.7025
RfactorNum. reflection% reflection
Rfree0.2556 3577 4.98 %
Rwork0.2184 --
obs0.2203 71826 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 46 394 7784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527598
X-RAY DIFFRACTIONf_angle_d0.661310356
X-RAY DIFFRACTIONf_chiral_restr0.04331122
X-RAY DIFFRACTIONf_plane_restr0.00471324
X-RAY DIFFRACTIONf_dihedral_angle_d8.28291018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.33041300.28222631X-RAY DIFFRACTION99.86
2.13-2.160.29391430.25322597X-RAY DIFFRACTION99.96
2.16-2.190.2861570.24162612X-RAY DIFFRACTION100
2.19-2.220.27961400.24652610X-RAY DIFFRACTION99.96
2.22-2.250.3691480.30292607X-RAY DIFFRACTION99.17
2.25-2.290.31951210.25982603X-RAY DIFFRACTION99.82
2.29-2.330.29851500.23552624X-RAY DIFFRACTION99.96
2.33-2.370.27811300.22412617X-RAY DIFFRACTION99.93
2.37-2.420.27111390.22072641X-RAY DIFFRACTION100
2.42-2.470.27131490.21812608X-RAY DIFFRACTION99.96
2.47-2.520.26671520.21872596X-RAY DIFFRACTION99.96
2.52-2.580.25711290.22242638X-RAY DIFFRACTION100
2.58-2.650.27521470.23022611X-RAY DIFFRACTION99.89
2.65-2.720.26361460.22442636X-RAY DIFFRACTION99.93
2.72-2.80.2651270.22022601X-RAY DIFFRACTION99.96
2.8-2.890.29391210.21992664X-RAY DIFFRACTION99.96
2.89-2.990.25851260.2252632X-RAY DIFFRACTION99.93
2.99-3.110.2731370.21192668X-RAY DIFFRACTION99.89
3.11-3.250.23271580.22192583X-RAY DIFFRACTION99.89
3.25-3.420.2521440.2192612X-RAY DIFFRACTION99.86
3.42-3.640.2311150.20572663X-RAY DIFFRACTION99.86
3.64-3.920.23681310.18832637X-RAY DIFFRACTION99.71
3.92-4.310.21071450.18472610X-RAY DIFFRACTION99.75
4.31-4.940.20811480.19222627X-RAY DIFFRACTION99.5
4.94-6.210.24541180.21392655X-RAY DIFFRACTION99.39
6.22-40.460.21341260.20942666X-RAY DIFFRACTION98.31
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)
11.246-0.368-0.2661.0450.0580.72-0.0419-0.189-0.069-0.00940.0780.0173-0.0016-0.0054-0.0120.07150.0117-0.01120.1330.0220.114135.5612.82774.019
20.926-0.083-0.250.897-0.1090.4320.0406-0.016-0.02720.00050.0220.0506-0.102-0.119-0.03940.09590.028-0.00710.1210.00050.114113.40523.29367.426
30.63-0.0592-0.00981.076-0.4270.991-0.0492-0.03870.0391-0.01110.0787-0.0127-0.0617-0.137-0.03080.1290.0303-0.0150.1390.00890.11398.75438.51494.493
40.391-0.261-0.03030.677-0.2291.096-0.125-0.13-0.03780.1350.0662-0.01740.0131-0.02040.02690.1630.03330.00480.1650.01540.111110.73119.428111.71
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2A302 - 492
3X-RAY DIFFRACTION3B0 - 261
4X-RAY DIFFRACTION4B262 - 492

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