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- PDB-4mlp: Mammalian cryptochrome in complex with a small molecule competito... -

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Basic information

Entry
Database: PDB / ID: 4mlp
TitleMammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
ComponentsCryptochrome-2
KeywordsTRANSCRIPTION / photolyase homology region / transcriptional repressor / PERIOD / FBXL3 / CLOCK / 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 / negative regulation of phosphoprotein phosphatase activity / entrainment of circadian clock by photoperiod / response to light stimulus / photoreceptor activity / phosphatase 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 / negative regulation of phosphoprotein phosphatase activity / entrainment of circadian clock by photoperiod / response to light stimulus / photoreceptor activity / phosphatase binding / response to insulin / FAD binding / response to activity / nuclear receptor binding / circadian regulation of gene expression / regulation of circadian rhythm / protein import into nucleus / circadian rhythm / single-stranded DNA binding / kinase binding / glucose homeostasis / protein-chromophore linkage / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / negative regulation of transcription, DNA-templated / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / FAD binding domain of DNA photolyase / Cryptochrome/DNA photolyase, FAD-binding domain / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / FAD binding domain of DNA photolyase / Cryptochrome/DNA photolyase, FAD-binding domain / 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-2CX / Cryptochrome-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.943 Å
AuthorsNangle, S. / Xing, W. / Zheng, N.
CitationJournal: Cell Res. / Year: 2013
Title: Crystal structure of mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase.
Authors: Nangle, S. / Xing, W. / Zheng, N.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cryptochrome-2
A: Cryptochrome-2
B: Cryptochrome-2
D: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,3508
Polymers234,7564
Non-polymers1,5944
Water27,9951554
1
C: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cryptochrome-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0882
Polymers58,6891
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)48.210, 93.651, 141.179
Angle α, β, γ (deg.)89.94, 90.09, 90.25
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cryptochrome-2 /


Mass: 58689.047 Da / Num. of mol.: 4 / Fragment: photolyase homology region UNP residues 1-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Chemical
ChemComp-2CX / N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide


Mass: 398.475 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1554 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES and 4-5% PEG8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 175262 / Num. obs: 170540 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 %
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.95-1.980.601195.1
1.98-2.020.496195
2.02-2.060.417195.7
2.06-2.10.369195.2
2.1-2.150.297196.3
2.15-2.20.239195.8
2.2-2.250.22196.4
2.25-2.310.18196.6
2.31-2.380.151196.8
2.38-2.460.131197.3
2.46-2.540.112197.4
2.54-2.650.099197.7
2.65-2.770.092197.9
2.77-2.910.081197.9
2.91-3.10.074198.3
3.1-3.330.068198.3
3.33-3.670.061198.5
3.67-4.20.054198.1
4.2-5.290.048198.1
5.29-500.045198.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I6J
Resolution: 1.943→44.458 Å / SU ML: 0.17 / σ(F): 0.08 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 1499 88 %random
Rwork0.1795 ---
obs0.1798 170540 --
all-175262 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.943→44.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16060 0 112 1554 17726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716656
X-RAY DIFFRACTIONf_angle_d1.08722612
X-RAY DIFFRACTIONf_dihedral_angle_d15.0946184
X-RAY DIFFRACTIONf_chiral_restr0.082320
X-RAY DIFFRACTIONf_plane_restr0.0042908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9433-2.0060.27151220.207613134X-RAY DIFFRACTION80
2.006-2.07770.25031250.205214782X-RAY DIFFRACTION90
2.0777-2.16090.24561360.198414908X-RAY DIFFRACTION91
2.1609-2.25920.20981290.190615265X-RAY DIFFRACTION93
2.2592-2.37840.24961430.191815386X-RAY DIFFRACTION94
2.3784-2.52730.23091330.185515704X-RAY DIFFRACTION95
2.5273-2.72250.20731420.189415700X-RAY DIFFRACTION96
2.7225-2.99640.23641410.18815973X-RAY DIFFRACTION97
2.9964-3.42980.2611410.184616058X-RAY DIFFRACTION98
3.4298-4.32060.19761410.159416032X-RAY DIFFRACTION98
4.3206-44.46940.17791460.168316099X-RAY DIFFRACTION98

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