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

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Basic information

Entry
Database: PDB / ID: 8rdp
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8a
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: 1.76 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)42,26111
Polymers41,1113
Non-polymers1,1508
Water1,58588
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0714
Polymers13,7041
Non-polymers3673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1434
Polymers13,7041
Non-polymers4393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0483
Polymers13,7041
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.356, 59.597, 87.875
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

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Protein , 1 types, 3 molecules ABC

#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

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Non-polymers , 5 types, 96 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1HZ7 / (5~{S})-3-(2-chlorophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione


Mass: 278.691 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.8 Å3/Da / Density % sol: 31.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM 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: 1.76→47.48 Å / Num. obs: 56873 / % possible obs: 100 % / Redundancy: 6.89 % / Biso Wilson estimate: 38.389 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.13 / Net I/σ(I): 8.06
Reflection shell

Rrim(I) all: 0.13 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible all
1.76-1.866.41.0492220.56299.8
5.24-47.487.0624.7421430.99799.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→47.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.071 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23045 1506 5 %RANDOM
Rwork0.18551 ---
obs0.18771 28622 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.359 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--3.35 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 1.76→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 66 88 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132616
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182258
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6413566
X-RAY DIFFRACTIONr_angle_other_deg1.4211.5735162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2935325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03219.706136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50715340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6521520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
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_it1.3261.8951288
X-RAY DIFFRACTIONr_mcbond_other1.3261.8941287
X-RAY DIFFRACTIONr_mcangle_it2.122.8221614
X-RAY DIFFRACTIONr_mcangle_other2.122.8231615
X-RAY DIFFRACTIONr_scbond_it1.8512.141328
X-RAY DIFFRACTIONr_scbond_other1.7982.1231325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8773.121946
X-RAY DIFFRACTIONr_long_range_B_refined5.24921.6912797
X-RAY DIFFRACTIONr_long_range_B_other5.20321.5682790
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)
11A30500.12
12B30500.12
21A28140.13
22C28140.13
31B27980.14
32C27980.14
LS refinement shellResolution: 1.76→1.803 Å
RfactorNum. reflection% reflection
Rfree0.277 103 -
Rwork0.296 2070 -
obs--99.68 %
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)
12.2563-0.00191.38441.44861.05174.12050.01680.0304-0.1532-0.03380.00150.02670.2037-0.0305-0.01830.1590.00950.0020.0107-0.03390.172118.96218.10432.4066
23.4467-0.83580.78362.3986-0.47052.17320.0127-0.0644-0.1268-0.0093-0.0050.0615-0.01180.044-0.00770.1607-0.00970.00850.00560.01770.119731.98797.582323.8051
32.41351.3565-0.05383.4814-0.24092.2577-0.0220.0079-0.0537-0.13490.08580.28520.1438-0.4056-0.06380.2702-0.01270.01330.1729-0.00930.266728.2565-6.5054-6.9449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 201
2X-RAY DIFFRACTION2B18 - 201
3X-RAY DIFFRACTION3C17 - 201

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