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

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Basic information

Entry
Database: PDB / ID: 8rdt
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8j
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: 1.95 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)42,0719
Polymers41,1113
Non-polymers9606
Water1,00956
1
A: Cereblon isoform 4
hetero molecules


  • defined by author
  • 14.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,1984
Polymers13,7041
Non-polymers4953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


  • defined by author
  • 14.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,1033
Polymers13,7041
Non-polymers4002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


  • defined by author
  • 13.8 kDa, 1 polymers
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)56.441, 59.488, 88.110
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-A1HZ2 / (5~{S})-3-(2,3,4-trimethoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione


Mass: 334.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O6 / 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.: 56 / 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: 1.8 Å3/Da / Density % sol: 31.79 %
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: Apr 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.303 Å / Num. obs: 41768 / % possible obs: 99.9 % / Redundancy: 7.01 % / Biso Wilson estimate: 45.965 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.106 / Net I/σ(I): 10.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.077.191.0567150.5241.81799.6
5.81-49.3036.7537.7115770.9990.04499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→49.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.775 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24169 1111 5 %RANDOM
Rwork0.19878 ---
obs0.20088 21143 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20 Å2
2--1.29 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 56 56 2387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132434
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182077
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6383310
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5744734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1125302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84620.083121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62415305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6691516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
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_it1.5993.271217
X-RAY DIFFRACTIONr_mcbond_other1.5973.2691216
X-RAY DIFFRACTIONr_mcangle_it2.3614.8951516
X-RAY DIFFRACTIONr_mcangle_other2.3614.8961517
X-RAY DIFFRACTIONr_scbond_it2.1843.5381217
X-RAY DIFFRACTIONr_scbond_other2.1263.5341214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3585.221789
X-RAY DIFFRACTIONr_long_range_B_refined4.87436.7832556
X-RAY DIFFRACTIONr_long_range_B_other4.87236.7382554
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)
11A29100.11
12B29100.11
21A23830.09
22C23830.09
31B24170.1
32C24170.1
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.288 78 -
Rwork0.291 1542 -
obs--99.39 %
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)
12.53440.03591.27782.10621.24265.18160.0520.0999-0.2318-0.08150.00880.07690.20540.1361-0.06070.01780.0067-0.00790.0064-0.01450.080719.202218.02131.4578
23.338-1.02550.78482.7378-0.54382.9587-0.00090.0071-0.0831-0.00950.02610.0661-0.00390.0304-0.02510.0030.00050.00480.00930.01590.035731.76857.578323.7701
33.38211.88930.59435.2373-0.20084.31130.02590.0013-0.1424-0.19560.03010.48080.3396-0.6379-0.0560.1378-0.03680.0420.2984-0.00860.250429.2136-6.5606-7.633
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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