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

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Basic information

Entry
Database: PDB / ID: 8rdr
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8g
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: 1.58 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)42,36511
Polymers41,1113
Non-polymers1,2548
Water2,504139
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1534
Polymers13,7041
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1534
Polymers13,7041
Non-polymers4503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0583
Polymers13,7041
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.663, 60.446, 88.841
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-A1HZ3 / (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione


Mass: 289.244 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H11N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.85 Å3/Da / Density % sol: 33.63 %
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 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→49.3 Å / Num. obs: 80830 / % possible obs: 100 % / Redundancy: 6.87 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.102 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all
1.58-1.686.851.1130730.5671.482
4.72-49.36.5132.5430270.9980.053

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.58→47.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.23 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 2127 5 %RANDOM
Rwork0.18273 ---
obs0.18427 40433 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.76 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.58→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 76 139 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132721
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172373
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.643718
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5735440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26619.507142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50115370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9161522
X-RAY DIFFRACTIONr_chiral_restr0.080.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
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_it1.1691.9551323
X-RAY DIFFRACTIONr_mcbond_other1.1691.9541322
X-RAY DIFFRACTIONr_mcangle_it1.8472.9251662
X-RAY DIFFRACTIONr_mcangle_other1.8472.9261663
X-RAY DIFFRACTIONr_scbond_it1.7282.1961398
X-RAY DIFFRACTIONr_scbond_other1.6992.1761391
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6913.1962037
X-RAY DIFFRACTIONr_long_range_B_refined5.17422.762943
X-RAY DIFFRACTIONr_long_range_B_other5.15422.5932932
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)
11A31110.13
12B31110.13
21A29020.13
22C29020.13
31B29880.14
32C29880.14
LS refinement shellResolution: 1.58→1.62 Å
RfactorNum. reflection% reflection
Rfree0.29 155 -
Rwork0.282 2945 -
obs--99.49 %
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)
11.7584-0.07060.86822.1361.13894.860.1140.1107-0.29450.0319-0.04680.16430.271-0.0113-0.06730.0180.0051-0.01720.0487-0.04110.069819.138918.15082.5776
23.1134-1.34610.12192.557-0.20692.1510.05420.0303-0.079-0.0670.02940.106-0.04340.0874-0.08370.0387-0.01610.01590.0102-0.00890.015532.17097.524324.0703
33.35811.54140.41493.5758-0.23762.7083-0.0314-0.0449-0.0675-0.170.06970.28560.2344-0.3625-0.03830.0967-0.0258-0.01320.13030.00840.077327.7985-6.213-6.9644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C18 - 201

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