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- PDB-7v8y: Crystal structure of mouse CRY2 in complex with SHP1703 compound -

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Basic information

Entry
Database: PDB / ID: 7v8y
TitleCrystal structure of mouse CRY2 in complex with SHP1703 compound
ComponentsCryptochrome-2
KeywordsCIRCADIAN CLOCK PROTEIN / circadian / clock / cryptochrome / CRY / CRY2
Function / homology
Function and homology information


regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding ...regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / FAD binding / response to activity / nuclear receptor binding / circadian regulation of gene expression / response to insulin / regulation of circadian rhythm / kinase binding / circadian rhythm / protein import into nucleus / glucose homeostasis / single-stranded DNA binding / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / negative regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-5YH / Cryptochrome-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiller, S.A. / Hirota, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H02402 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy.
Authors: Miller, S. / Kesherwani, M. / Chan, P. / Nagai, Y. / Yagi, M. / Cope, J. / Tama, F. / Kay, S.A. / Hirota, T.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1932
Polymers58,8471
Non-polymers3451
Water4,774265
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 area21080 Å2
Unit cell
Length a, b, c (Å)77.737, 77.737, 159.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Cryptochrome-2


Mass: 58847.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Chemical ChemComp-5YH / 1-[(2R)-3-[3,6-bis(fluoranyl)carbazol-9-yl]-2-oxidanyl-propyl]imidazolidin-2-one


Mass: 345.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F2N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 0.15 M NaCl, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→67.18 Å / Num. obs: 42509 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 29.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.013 / Rrim(I) all: 0.061 / Net I/σ(I): 29.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 19.9 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 6 / Num. unique obs: 6134 / CC1/2: 0.971 / Rpim(I) all: 0.112 / Rrim(I) all: 0.509 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.8.0257refinement
xia2data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX8

6kx8


Resolution: 1.9→38.87 Å / SU ML: 0.1726 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.79
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 2080 4.9 %
Rwork0.1664 40358 -
obs0.1683 42438 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 25 265 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013966
X-RAY DIFFRACTIONf_angle_d1.00055422
X-RAY DIFFRACTIONf_chiral_restr0.0603577
X-RAY DIFFRACTIONf_plane_restr0.0067700
X-RAY DIFFRACTIONf_dihedral_angle_d21.7223543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.24551400.18252653X-RAY DIFFRACTION98.66
1.95-20.2061160.17262683X-RAY DIFFRACTION99.5
2-2.050.22341410.16522688X-RAY DIFFRACTION99.89
2.05-2.110.20451640.16442663X-RAY DIFFRACTION100
2.11-2.180.22181270.16012688X-RAY DIFFRACTION100
2.18-2.260.20791480.1622683X-RAY DIFFRACTION100
2.26-2.350.19961370.16952693X-RAY DIFFRACTION100
2.35-2.450.22571610.16942676X-RAY DIFFRACTION100
2.45-2.580.20741280.15992708X-RAY DIFFRACTION100
2.58-2.750.21191540.17132678X-RAY DIFFRACTION100
2.75-2.960.21291490.18292672X-RAY DIFFRACTION99.96
2.96-3.250.21771070.182739X-RAY DIFFRACTION100
3.26-3.730.22051450.17472695X-RAY DIFFRACTION100
3.73-4.690.18421410.15012693X-RAY DIFFRACTION100
4.69-38.870.19171220.16092746X-RAY DIFFRACTION99.69
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)
11.26049865394-0.02568256724860.3124155095820.4721128123440.1387229072370.706074212526-0.0819987866660.01830032258230.1281284951690.04916120429020.00624386368166-0.0909776950919-0.06955869994570.0529171907239-0.0002907071727290.277763908579-0.0336037573038-0.06528377025580.1680013861750.02456799683140.2350096817758.6049924154342.889849101-8.48014292522
21.195467982120.3979580325510.1616157121880.94609511516-0.0468062289320.4571404853550.0559516894593-0.0426467703457-0.2152698050140.0972294466874-0.02023361742360.02525538686010.0711975806392-0.1291673823830.005210916924780.310301242714-0.0589074774189-0.0502804645780.2066635182930.02801722355570.224374815313-9.9344725224922.5249247708-8.99174588631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 279 )
2X-RAY DIFFRACTION2chain 'A' and (resid 280 through 510 )

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