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- PDB-7d0m: Crystal structure of mouse CRY1 with bound cryoprotectant -

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Basic information

Entry
Database: PDB / ID: 7d0m
TitleCrystal structure of mouse CRY1 with bound cryoprotectant
ComponentsCryptochrome-1
KeywordsCIRCADIAN CLOCK PROTEIN / CRY / CRY1 / cryptochrome / PHR
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
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
DI(HYDROXYETHYL)ETHER / Cryptochrome-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMiller, S.A. / Aikawa, Y. / Hirota, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR14LA Japan
Japan Society for the Promotion of Science (JSPS)15H05590 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.
Authors: Miller, S. / Srivastava, A. / Nagai, Y. / Aikawa, Y. / Tama, F. / Hirota, T.
History
DepositionSep 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6723
Polymers57,3721
Non-polymers3002
Water8,017445
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 area740 Å2
ΔGint7 kcal/mol
Surface area21440 Å2
Unit cell
Length a, b, c (Å)45.057, 77.507, 134.500
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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→67.25 Å / Num. obs: 35031 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 14.94 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.062 / Rrim(I) all: 0.153 / Net I/σ(I): 8.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5000 / CC1/2: 0.908 / Rpim(I) all: 0.22 / Rrim(I) all: 0.544 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5.8.0257refinement
xia20.6.467data reduction
SCALA3.3.22data scaling
PHASER2.8.3phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KX4

6kx4


Resolution: 1.95→67.25 Å / SU ML: 0.1769 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7862
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 1789 5.13 %
Rwork0.177 33072 -
obs0.1787 34861 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.55 Å2
Refinement stepCycle: LAST / Resolution: 1.95→67.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 20 445 4340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00454006
X-RAY DIFFRACTIONf_angle_d0.70745456
X-RAY DIFFRACTIONf_chiral_restr0.0466585
X-RAY DIFFRACTIONf_plane_restr0.0046702
X-RAY DIFFRACTIONf_dihedral_angle_d21.197554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.23611350.20522413X-RAY DIFFRACTION97.21
2-2.060.23771350.19372505X-RAY DIFFRACTION98.54
2.06-2.130.24951190.18562512X-RAY DIFFRACTION98.5
2.13-2.20.22171390.17852465X-RAY DIFFRACTION98.38
2.2-2.290.23321430.17952521X-RAY DIFFRACTION98.7
2.29-2.390.23151180.18212520X-RAY DIFFRACTION98.47
2.4-2.520.23961430.18882512X-RAY DIFFRACTION98.66
2.52-2.680.24431340.192549X-RAY DIFFRACTION99.37
2.68-2.890.20421460.19562552X-RAY DIFFRACTION99.48
2.89-3.180.26861520.19262550X-RAY DIFFRACTION99.7
3.18-3.640.17741400.16852586X-RAY DIFFRACTION99.82
3.64-4.580.15691500.14182633X-RAY DIFFRACTION99.75
4.58-67.250.18761350.16982754X-RAY DIFFRACTION99.35
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)
10.351422647013-0.0110281830116-0.1159281158940.854443924114-0.2142349811540.8767122765250.00728928004464-0.0134477591104-0.01997721693110.0736247778375-0.006388961499880.009922845477870.0340930153585-0.03269344106660.004346564171330.0548380568299-0.0105749653104-0.006968316306230.08455087751920.0002249052761790.0672083606899-3.705259614298.51912620214-13.650123439
20.398732096410.1428668870170.2010352957030.4459532133170.1449217683390.6347029448020.01208568336070.0582546637852-0.00358969637771-0.05729467372090.000381981894304-0.00920471944768-0.0272557687287-0.0279607719614-0.02677635700360.05829472505670.01252944241840.001456728587610.06863072957280.006646943121290.0677066384926-6.41233635517.4399778825-38.9690888462
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 261 )2 - 2611 - 260
22chain 'A' and (resid 262 through 495 )262 - 495261 - 494

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