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- PDB-8rdq: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 8rdq
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8b
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE / spiro-isoxazole
Function / homologyCULT domain / CULT domain profile. / metal ion binding / PHOSPHATE ION / : / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsBischof, L. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode.
Authors: Shevalev, R. / Bischof, L. / Sapegin, A. / Bunev, A. / Olga, G. / Kantin, G. / Kalinin, S. / Hartmann, M.D.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cereblon isoform 4
B: Cereblon isoform 4
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0289
Polymers41,1113
Non-polymers9176
Water93752
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1774
Polymers13,7041
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0823
Polymers13,7041
Non-polymers3792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7692
Polymers13,7041
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.536, 59.800, 88.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein Cereblon isoform 4


Mass: 13703.577 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4TVL0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YQO / (5S)-3-(2,4-dichlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione


Mass: 313.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.81 Å3/Da / Density % sol: 32.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3 mM thalidomide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0001 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.03→47.61 Å / Num. obs: 263076 / % possible obs: 99.9 % / Redundancy: 7.06 % / Biso Wilson estimate: 43.893 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.163 / Net I/σ(I): 8.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.03-2.157.241.0360320.5291.84999.7
6.04-47.617.332.7714020.9980.05599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.03→47.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.2 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24929 999 5 %RANDOM
Rwork0.20509 ---
obs0.20724 18897 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.255 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20 Å2
2--0.52 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.03→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 48 52 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132431
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182089
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6393304
X-RAY DIFFRACTIONr_angle_other_deg1.2521.5774758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69519.837123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02315307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461517
X-RAY DIFFRACTIONr_chiral_restr0.060.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
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_it0.9332.4181206
X-RAY DIFFRACTIONr_mcbond_other0.9332.4171205
X-RAY DIFFRACTIONr_mcangle_it1.5383.6121497
X-RAY DIFFRACTIONr_mcangle_other1.5383.6121498
X-RAY DIFFRACTIONr_scbond_it1.3842.6291225
X-RAY DIFFRACTIONr_scbond_other1.3082.6221222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1693.8851802
X-RAY DIFFRACTIONr_long_range_B_refined4.13327.3172564
X-RAY DIFFRACTIONr_long_range_B_other4.1327.2682562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A28610.11
12B28610.11
21A24700.1
22C24700.1
31B25310.1
32C25310.1
LS refinement shellResolution: 2.03→2.082 Å
RfactorNum. reflection% reflection
Rfree0.301 72 -
Rwork0.303 1371 -
obs--99.45 %
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)
13.08680.0251.57422.29761.26964.69550.06780.1071-0.2526-0.07450.00940.02750.16910.0482-0.07720.12880.0136-0.00460.1369-0.03980.028719.167318.28012.0532
23.8898-1.01940.53783.2868-0.6942.35740.0273-0.0302-0.12690.02660.02990.0703-0.03530.0391-0.05720.1411-0.0140.00440.10920.01930.008731.98397.500323.7777
33.10981.64080.16374.9305-0.56722.4177-0.0106-0.0497-0.0997-0.26680.08750.49790.2797-0.5174-0.07690.318-0.03890.03850.3978-0.01660.207128.8195-6.2799-7.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C18 - 150

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