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- PDB-4tzc: Crystal Structure of Murine Cereblon in Complex with Thalidomide -

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Basic information

Entry
Database: PDB / ID: 4tzc
TitleCrystal Structure of Murine Cereblon in Complex with Thalidomide
ComponentsProtein cereblon
KeywordsLIGASE / Ubiquitin ligase / DCAF
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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Peptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain ...Peptide methionine sulfoxide reductase. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / 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
S-Thalidomide / Protein cereblon
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 Å
AuthorsChamberlain, P.P. / Pagarigan, B. / Delker, S. / Leon, B.
CitationJournal: to be published
Title: Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex
Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Leon, B. / Rychak, E. / Corral, L. / Ren, Y. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / ...Authors: Chamberlain, P.P. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Leon, B. / Rychak, E. / Corral, L. / Ren, Y. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / Mori, T. / Hirano, Y. / Handa, H. / Hakoshima, T. / Daniel, T.O. / Cathers, B.E.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Protein cereblon
A: Protein cereblon
B: Protein cereblon
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,29520
Polymers48,2324
Non-polymers2,06316
Water6,575365
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5745
Polymers12,0581
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6706
Polymers12,0581
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3823
Polymers12,0581
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6706
Polymers12,0581
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.146, 143.146, 143.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-617-

HOH

21B-618-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein
Protein cereblon / Protein PiL


Mass: 12057.911 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EF2 / S-Thalidomide


Mass: 258.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100mM Sodium Acetate pH 5, 600-800mM Ammonium Sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 76864 / % possible obs: 99.9 % / Redundancy: 22.8 % / Rmerge(I) obs: 0.089 / Χ2: 1.019 / Net I/av σ(I): 38.415 / Net I/σ(I): 9.7 / Num. measured all: 1750335
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.88-1.95230.59976521.049100
1.95-2.0323.10.36777391.012100
2.03-2.1223.20.27876421.002100
2.12-2.2322.80.21376711.042100
2.23-2.3720.50.17477471.006100
2.37-2.5523.40.14776871.008100
2.55-2.8123.50.10576781.009100
2.81-3.2123.50.07776841.025100
3.21-4.0521.50.06776611.01899.5
4.05-5023.30.04977031.018100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.102 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21973 1983 5 %RANDOM
Rwork0.17289 ---
obs0.1752 37584 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.609 Å2
Refinement stepCycle: 1 / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 120 365 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9754493
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.9265392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8923.661112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70215551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.263158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212376
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.882→1.931 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 137 -
Rwork0.261 2673 -
obs--99.96 %
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)
10.58210.37660.05630.39130.16620.4360.02060.0632-0.04430.04270.0684-0.03050.00750.0193-0.08890.0271-0.00990.00380.0424-0.01480.036817.1956-28.2482-62.635
20.3542-0.00910.06740.8481-0.36760.35630.01470.08290.01660.02270.03630.0218-0.05630.0244-0.0510.0406-0.0326-0.01280.05970.02870.037454.0351-43.1541-62.3951
30.56960.3169-0.270.3438-0.00230.48130.0639-0.02320.00940.0172-0.0292-0.016-0.05470.0396-0.03470.0392-0.02790.01750.0347-0.00830.01728.2151-9.4812-54.5747
40.1872-0.07630.14070.8453-0.32580.3068-0.0274-0.0583-0.0312-0.01120.0328-0.02380.0096-0.0054-0.00540.02470.0220.00580.03830.01980.031853.7868-26.212-78.2029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 426
2X-RAY DIFFRACTION2B321 - 427
3X-RAY DIFFRACTION3C320 - 426
4X-RAY DIFFRACTION4D321 - 427

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