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- PDB-3wx1: Mouse Cereblon thalidomide binding domain, selenomethionine derivative -

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Basic information

Entry
Database: PDB / ID: 3wx1
TitleMouse Cereblon thalidomide binding domain, selenomethionine derivative
ComponentsProtein cereblon
KeywordsMETAL BINDING PROTEIN / Zinc Finger / E3 ubiquitin ligase
Function / homology
Function and homology information


negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination ...negative regulation of large conductance calcium-activated potassium channel activity / negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain ...Peptide methionine sulfoxide reductase. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / CULT domain / CULT domain profile. / Lon protease, N-terminal domain superfamily / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsMori, T. / Ito, T. / Hirano, Y. / Yamaguchi, Y. / Handa, H. / Hakoshima, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs
Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Chie-Leon, B. / Rychak, E. / Corral, L.G. / Ren, Y.J. / Wang, M. / Riley, M. / Delker, S.L. / Ito, T. / Ando, ...Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Chie-Leon, B. / Rychak, E. / Corral, L.G. / Ren, Y.J. / Wang, M. / Riley, M. / Delker, S.L. / Ito, T. / Ando, H. / Mori, T. / Hirano, Y. / Handa, H. / Hakoshima, T. / Daniel, T.O. / Cathers, B.E.
History
DepositionJul 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3738
Polymers24,8582
Non-polymers5156
Water2,306128
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6874
Polymers12,4291
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6874
Polymers12,4291
Non-polymers2583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.112, 118.112, 118.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-502-

SO4

21A-502-

SO4

31B-502-

SO4

41B-502-

SO4

51A-607-

HOH

61B-648-

HOH

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Components

#1: Protein Protein cereblon / Protein PiL


Mass: 12429.062 Da / Num. of mol.: 2 / Fragment: Cereblon(CRBN), UNP residues 322-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crbn / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C7D2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.7
Details: 0.1M sodium acetate (pH 5.7), 0.2M sodium sulphate, 12% PEG3350, 30% glycerol, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97911, 0.99513, 0.97941
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 26, 2011
RadiationScattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.995131
30.979411
ReflectionResolution: 1.93→50 Å / Num. all: 20774 / Num. obs: 20774 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.93→34.1 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.183 / SU ML: 0.092 / ESU R: 0.139 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21224 1066 5.1 %RANDOM
Rwork0.18935 ---
obs0.19057 19657 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.317 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 22 128 1762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191675
X-RAY DIFFRACTIONr_bond_other_d00.021559
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.9572279
X-RAY DIFFRACTIONr_angle_other_deg2.36233612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.81623.62158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03215264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.025154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211817
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02377
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5313.904825
X-RAY DIFFRACTIONr_mcbond_other2.5313.901824
X-RAY DIFFRACTIONr_mcangle_it3.5955.8221026
X-RAY DIFFRACTIONr_mcangle_other3.5945.8251027
X-RAY DIFFRACTIONr_scbond_it4.4074.327850
X-RAY DIFFRACTIONr_scbond_other4.3114.33835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7516.341230
X-RAY DIFFRACTIONr_long_range_B_refined7.4632.4021853
X-RAY DIFFRACTIONr_long_range_B_other7.34732.1691820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.929→1.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 67 -
Rwork0.246 1453 -
obs--99.61 %

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