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- PDB-4i6e: A vertebrate cryptochrome -

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Basic information

Entry
Database: PDB / ID: 4i6e
TitleA vertebrate cryptochrome
ComponentsCryptochrome-2
KeywordsTRANSCRIPTION / Cryptochrome Circadian Clock / Photolyase fold / Circadian Clock / FAD / Nucleus
Function / homology
Function and homology information


regulation of sodium-dependent phosphate transport / 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 ...regulation of sodium-dependent phosphate transport / 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 / protein import into nucleus / circadian rhythm / 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
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: 2.7 Å
AuthorsXing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
CitationJournal: Nature / Year: 2013
Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket.
Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Sep 20, 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-2


Theoretical massNumber of molelcules
Total (without water)58,6891
Polymers58,6891
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.935, 68.935, 127.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cryptochrome-2 /


Mass: 58689.047 Da / Num. of mol.: 1 / Fragment: UNP residues 1-512
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-imadzole, pH6.5, 7.2% PEG8000, 20% Ethylene glycol (v/v), 0.03M NaF,NaBr,NaI, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 16379 / Num. obs: 16379 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 45.023
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 7.579 / Num. unique all: 815 / Rsym value: 0.191 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CVU

3cvu


Resolution: 2.7→48.744 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 32.72 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1377 8.41 %Random
Rwork0.2438 ---
all0.2475 16379 --
obs0.2475 16379 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 0 1 3822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093928
X-RAY DIFFRACTIONf_angle_d1.2725323
X-RAY DIFFRACTIONf_dihedral_angle_d16.8461443
X-RAY DIFFRACTIONf_chiral_restr0.09557
X-RAY DIFFRACTIONf_plane_restr0.005682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79660.39811390.29781496X-RAY DIFFRACTION100
2.7966-2.90860.34041410.29241511X-RAY DIFFRACTION100
2.9086-3.04090.36611370.27351491X-RAY DIFFRACTION100
3.0409-3.20120.3191390.2611467X-RAY DIFFRACTION100
3.2012-3.40170.3231340.26021503X-RAY DIFFRACTION100
3.4017-3.66430.31261310.24911518X-RAY DIFFRACTION100
3.6643-4.03290.28751380.23061493X-RAY DIFFRACTION100
4.0329-4.61610.29771400.23011493X-RAY DIFFRACTION100
4.6161-5.81430.21851370.24421509X-RAY DIFFRACTION100
5.8143-48.75230.26031410.22541521X-RAY DIFFRACTION100
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)
11.53050.6-0.26992.1217-1.39910.92090.43231.0060.2897-0.2503-0.31510.597-0.7262-0.6636-0.2731.11690.8557-0.32.2909-0.85641.352563.3936-26.3223-3.7209
27.8445-2.8014-0.18342.4808-0.75670.50670.0077-0.18530.1199-0.2264-0.40371.0044-1.3581-1.16570.28720.95530.4933-0.09861.1943-0.35980.80473.8237-26.90236.0558
31.34110.37460.53720.8609-0.20291.39080.04710.7866-0.35620.1495-0.9341.3221-0.8429-2.16250.30770.5470.6704-0.33512.5128-0.95811.70464.1448-34.5468-2.3906
41.7122-0.453-0.91623.72950.09770.92930.87530.67940.3581-0.34660.06830.52250.01760.1487-0.2971.38221.2454-0.26911.3742-0.50521.519962.9403-14.0609-1.6101
53.6643-0.2532-2.80291.9749-1.57345.13210.55430.93941.0383-0.9358-0.4871-0.0488-1.3781-0.9491-0.01961.38180.3203-0.1650.6595-0.0150.814984.0182-23.1993-3.2087
60.0103-0.014-0.01310.00410.01050.0164-0.0810.5662-0.1312-0.81770.11980.0521-0.0131-0.26680.00631.9165-0.1922-0.02652.64980.00450.98882.7879-28.3897-27.3243
72.41781.79861.19833.98072.03061.0836-0.25351.3515-0.3367-1.6502-0.78340.5056-1.871-1.57080.61831.36420.6451-0.38332.004-0.35331.02575.1264-36.2777-18.2441
84.1002-0.3661-0.01125.72142.15785.86860.20910.1105-0.83020.4642-0.26030.44030.5715-1.02520.00980.4344-0.0480.01210.53-0.09750.623387.6985-47.8185-2.8722
95.5529-0.68250.62923.25290.1045.02260.08740.88520.00570.08630.4927-0.4920.02470.9729-0.38950.5956-0.1870.18890.8703-0.42250.878102.5294-44.966-13.6686
106.41712.1631-2.00522.9287-1.41014.4864-0.2684-0.608-0.6637-0.01140.4157-0.43270.94740.4885-0.09980.7960.2681-0.23370.8052-0.22431.1713102.3309-55.0946-5.806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 21:42)
2X-RAY DIFFRACTION2(chain A and resid 43:71)
3X-RAY DIFFRACTION3(chain A and resid 72:183)
4X-RAY DIFFRACTION4(chain A and resid 184:209)
5X-RAY DIFFRACTION5(chain A and resid 210:241)
6X-RAY DIFFRACTION6(chain A and resid 242:258)
7X-RAY DIFFRACTION7(chain A and resid 259:320)
8X-RAY DIFFRACTION8(chain A and resid 321:423)
9X-RAY DIFFRACTION9(chain A and resid 424:469)
10X-RAY DIFFRACTION10(chain A and resid 470:510)

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