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- PDB-5t5x: High resolution structure of mouse Cryptochrome 1 -

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Basic information

Entry
Database: PDB / ID: 5t5x
TitleHigh resolution structure of mouse Cryptochrome 1
ComponentsCryptochrome-1
KeywordsTRANSCRIPTION / repressor / circadian
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 / E-box binding / entrainment of circadian clock by photoperiod ...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 / E-box binding / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding / signal transduction in response to DNA damage / negative regulation of gluconeogenesis / 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 / histone deacetylase binding / circadian rhythm / 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 / cytoplasm / cytosol
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMichael, A.K. / Tripathi, S. / Partch, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107069 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA189660 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Authors: Michael, A.K. / Fribourgh, J.L. / Chelliah, Y. / Sandate, C.R. / Hura, G.L. / Schneidman-Duhovny, D. / Tripathi, S.M. / Takahashi, J.S. / Partch, C.L.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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)56,6272
Polymers56,5921
Non-polymers351
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.630, 51.035, 54.175
Angle α, β, γ (deg.)71.62, 84.12, 88.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cryptochrome-1


Mass: 56591.879 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.8, 10 mM EDTA, 15% v/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→51.15 Å / Num. obs: 38528 / % possible obs: 93.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 45.4
Reflection shellResolution: 1.79→1.86 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K0R

4k0r


Resolution: 1.84→48.428 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1840 5.14 %
Rwork0.1676 --
obs0.1709 35812 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→48.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 1 455 4270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133935
X-RAY DIFFRACTIONf_angle_d1.3475335
X-RAY DIFFRACTIONf_dihedral_angle_d14.7821459
X-RAY DIFFRACTIONf_chiral_restr0.053563
X-RAY DIFFRACTIONf_plane_restr0.008684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.88980.33261260.2312611X-RAY DIFFRACTION92
1.8898-1.94540.27171300.21142563X-RAY DIFFRACTION92
1.9454-2.00820.27161710.19042561X-RAY DIFFRACTION93
2.0082-2.07990.25791480.18572614X-RAY DIFFRACTION93
2.0799-2.16320.24971310.17822596X-RAY DIFFRACTION93
2.1632-2.26170.27061390.16952607X-RAY DIFFRACTION93
2.2617-2.38090.26381220.16862626X-RAY DIFFRACTION94
2.3809-2.53010.23311310.15872637X-RAY DIFFRACTION93
2.5301-2.72540.24611360.16192628X-RAY DIFFRACTION94
2.7254-2.99960.19631400.16972601X-RAY DIFFRACTION93
2.9996-3.43360.22381460.15722641X-RAY DIFFRACTION95
3.4336-4.32550.19681550.14442644X-RAY DIFFRACTION95
4.3255-48.44520.20761650.16322643X-RAY DIFFRACTION96

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