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- PDB-4tzu: Crystal Structure of Murine Cereblon in Complex with Pomalidomide -

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Basic information

Entry
Database: PDB / ID: 4tzu
TitleCrystal Structure of Murine Cereblon in Complex with Pomalidomide
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-Pomalidomide / Protein cereblon
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / Mori, T. / Handa, H. / Hakoshima, T. / Daniel, T.O. / Cathers, B.E. / Lopez-Girona, A. / Miller, K. / Carmel, G. ...Authors: Chamberlain, P.P. / Wang, M. / Riley, M. / Delker, S. / Ito, T. / Hideki, A. / Mori, T. / Handa, H. / Hakoshima, T. / Daniel, T.O. / Cathers, B.E. / Lopez-Girona, A. / Miller, K. / Carmel, G. / Pagarigan, B. / Leon, B. / Rychak, E. / Corral, L. / Ren, Y.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site_anisotrop / citation ...atom_site_anisotrop / citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id ..._atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,45920
Polymers48,3364
Non-polymers2,12316
Water3,261181
1
A: Protein cereblon
B: Protein cereblon
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,84415
Polymers36,2523
Non-polymers1,59212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-93 kcal/mol
Surface area13350 Å2
MethodPISA
2
C: Protein cereblon
hetero molecules

C: Protein cereblon
hetero molecules

C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,84415
Polymers36,2523
Non-polymers1,59212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_445-z-1,-x-1,y1
crystal symmetry operation10_454-y-1,z,-x-11
Buried area4970 Å2
ΔGint-132 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.340, 143.340, 143.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11C-610-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPRODD321 - 4261 - 106
21PROPROAA321 - 4261 - 106
12LEULEUDD321 - 4251 - 105
22LEULEUBB321 - 4251 - 105
13PROPRODD321 - 4261 - 106
23PROPROCC321 - 4261 - 106
14LEULEUAA321 - 4251 - 105
24LEULEUBB321 - 4251 - 105
15PROPROAA321 - 4261 - 106
25PROPROCC321 - 4261 - 106
16LEULEUBB321 - 4251 - 105
26LEULEUCC321 - 4251 - 105

NCS ensembles :
ID
1
2
3
4
5
6
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Protein cereblon / Protein PiL


Mass: 12083.990 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-Y70 / S-Pomalidomide


Mass: 273.244 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H11N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100mM Sodium Acetate pH5, 600-800mM Ammonium Sulfate.

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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: Aug 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→101.357 Å / Num. all: 30305 / Num. obs: 30305 / % possible obs: 92.3 % / Redundancy: 2.9 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Rsym value: 0.074 / Net I/av σ(I): 2.99 / Net I/σ(I): 10.1 / Num. measured all: 88108
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.112.90.2042.11296844130.1340.2045.492.4
2.11-2.2430.1414.41234241760.0910.141792.8
2.24-2.392.90.1670.91141639180.1210.1678.592.2
2.39-2.582.90.0896.51087637050.0590.0899.793.4
2.58-2.832.90.0742.9978533940.0510.07411.393.1
2.83-3.162.90.0589.7885130550.0380.05812.892.8
3.16-3.652.80.0647.9771527310.0410.06413.692.8
3.65-4.472.70.0635.6616622430.0430.06313.990.9
4.47-6.322.90.0545512417370.0360.05414.389.9
6.32-41.3793.10.0962.828659330.0660.09614.386.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.668 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1536 5.1 %RANDOM
Rwork0.1956 28750 --
obs0.1979 30286 91.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.65 Å2 / Biso mean: 22.241 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: final / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 124 181 3156
Biso mean--37.04 35.64 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193050
X-RAY DIFFRACTIONr_angle_refined_deg1.711.9314153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.0695355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.53123.905105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.686158
X-RAY DIFFRACTIONr_chiral_restr0.110.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0212180
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D1210.06
12A1210.06
21D1160.07
22B1160.07
31D1120.06
32C1120.06
41A1200.07
42B1200.07
51A1200.06
52C1200.06
61B1160.05
62C1160.05
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 111 -
Rwork0.196 2036 -
all-2147 -
obs--91.32 %
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)
12.0366-1.0859-0.3181.23330.45281.52930.0287-0.0670.0883-0.06870.1421-0.0696-0.02440.0587-0.17090.04410.0217-0.00260.0613-0.030.0426-54.6516-43.2209-9.1362
21.3609-0.78510.69411.17660.1631.89030.14340.0596-0.0559-0.1342-0.0514-0.07630.08550.1629-0.0920.09730.0656-0.03450.0567-0.02220.0457-43.1673-61.854-17.2054
31.1560.00540.47061.45980.16642.01980.0510.2229-0.0854-0.1759-0.09770.25630.18480.09790.04670.09840.0354-0.08060.0849-0.05750.1052-62.7073-54.8741-27.4069
42.1972-0.09391.04052.85850.10232.2728-0.0824-0.1918-0.12450.12420.0367-0.2250.05490.15550.04570.05080.0048-0.05410.12510.08010.1277-82.0343-54.6468-42.6005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D321 - 426
2X-RAY DIFFRACTION2A321 - 426
3X-RAY DIFFRACTION3B321 - 427
4X-RAY DIFFRACTION4C321 - 426

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