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

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Basic information

Entry
Database: PDB / ID: 8rds
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with spiro-isoxazol based compound 8i
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 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

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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)41,9509
Polymers41,1113
Non-polymers8406
Water73941
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1384
Polymers13,7041
Non-polymers4353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0433
Polymers13,7041
Non-polymers3402
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)56.385, 59.297, 86.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-A1HZ6 / (5~{S})-3-(2-methoxyphenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione


Mass: 274.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O4 / 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.: 41 / 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: 1.75 Å3/Da / Density % sol: 29.94 %
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 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2→48.86 Å / Num. obs: 37772 / % possible obs: 100 % / Redundancy: 7.02 % / Biso Wilson estimate: 48.99 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.103 / Net I/σ(I): 10.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.127.11.1161350.5121.57299.9
5.96-48.866.7336.4814290.9980.04499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→48.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.329 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25337 1012 5 %RANDOM
Rwork0.20659 ---
obs0.20883 19158 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0 Å2
2---2.77 Å20 Å2
3---3.15 Å2
Refinement stepCycle: 1 / Resolution: 2→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 48 41 2083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181825
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6392882
X-RAY DIFFRACTIONr_angle_other_deg1.2281.5794167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26519.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65415278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.161516
X-RAY DIFFRACTIONr_chiral_restr0.0540.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
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_it1.1483.2021062
X-RAY DIFFRACTIONr_mcbond_other1.1483.2021061
X-RAY DIFFRACTIONr_mcangle_it1.894.7891317
X-RAY DIFFRACTIONr_mcangle_other1.894.7891318
X-RAY DIFFRACTIONr_scbond_it1.5133.3861066
X-RAY DIFFRACTIONr_scbond_other1.473.3781063
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3615.011560
X-RAY DIFFRACTIONr_long_range_B_refined4.3935.6032208
X-RAY DIFFRACTIONr_long_range_B_other4.38435.572207
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2847 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.051 Å
RfactorNum. reflection% reflection
Rfree0.34 80 -
Rwork0.303 1398 -
obs--99.73 %
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)
12.73410.32161.26741.95011.63644.36720.01710.1253-0.1796-0.03060.03710.01860.11820.0435-0.05410.05760.0115-0.00530.1642-0.02920.016219.285118.08171.5714
23.2118-1.6820.34754.3347-0.85732.5833-0.0247-0.0227-0.08280.0721-0.0129-0.0320.04190.08550.03760.0759-0.0213-0.00090.14570.0240.007631.90568.406323.5801
34.7087-1.6252-0.1946.31831.1064.1829-0.12330.2128-0.5819-0.0998-0.3040.97520.3959-0.55280.42720.2864-0.070.11030.421-0.10220.384631.8372-2.9534-6.6747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C18 - 201

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