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- PDB-9htk: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 9htk
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2n
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE
Function / homologyCULT domain / CULT domain profile. / metal ion binding / : / : / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.49 Å
AuthorsBischof, L. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Extending the chemical space of glutarimide-based cereblon ligands through an efficient Rh(II)-catalyzed X-H insertion reaction.
Authors: Levashova, E. / Bischof, L. / Bunev, A. / Sapegin, A. / Grygor'eva, O. / Kudinov, A. / Ebeling, S. / Tatarinov, I. / Dar'in, D. / Kantin, G. / Hartmann, M.D. / Kalinin, S.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: 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)41,9719
Polymers41,1113
Non-polymers8606
Water2,450136
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,7041
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,7041
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9903
Polymers13,7041
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.609, 59.756, 88.464
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-A1IXA / (3S)-3-phenylsulfanylpiperidine-2,6-dione


Mass: 221.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1I4R / (3R)-3-phenylsulfanylpiperidine-2,6-dione


Mass: 221.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.82 Å3/Da / Density % sol: 32.41 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 49304 / % possible obs: 99.6 % / Redundancy: 12.88 % / Biso Wilson estimate: 27.73 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.32
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 12.44 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 7710 / CC1/2: 0.638 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.49→41.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.534 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21003 2465 5 %RANDOM
Rwork0.17596 ---
obs0.17763 46839 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20 Å2
2--0.62 Å2-0 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.49→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 48 136 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132742
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172396
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6413746
X-RAY DIFFRACTIONr_angle_other_deg1.4971.5765484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7925352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09319.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6251523
X-RAY DIFFRACTIONr_chiral_restr0.0880.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
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_it1.0481.5811363
X-RAY DIFFRACTIONr_mcbond_other1.0481.581362
X-RAY DIFFRACTIONr_mcangle_it1.7022.3671727
X-RAY DIFFRACTIONr_mcangle_other1.7012.3671728
X-RAY DIFFRACTIONr_scbond_it1.6041.7621379
X-RAY DIFFRACTIONr_scbond_other1.6031.7631380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4752.5832019
X-RAY DIFFRACTIONr_long_range_B_refined4.50718.0712917
X-RAY DIFFRACTIONr_long_range_B_other4.48517.9652909
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)
11A32070.12
12B32070.12
21A30140.15
22C30140.15
31B28560.15
32C28560.15
LS refinement shellResolution: 1.492→1.531 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 167 -
Rwork0.313 3248 -
obs--95.07 %
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)
11.7933-0.07530.77321.41911.01173.73460.04820.0539-0.1954-0.0444-0.0120.04590.244-0.0127-0.03620.02890.0053-0.01060.0263-0.02580.051619.115217.86282.6974
22.8288-0.99450.28062.1877-0.4241.87570.0092-0.0148-0.1051-0.0552-0.00390.0911-0.0030.0151-0.00540.0037-0.0015-0.00080.00690.00530.012432.08727.599723.9516
32.66121.42210.4853.42190.02622.57060.0298-0.0327-0.049-0.11590.03240.32080.1789-0.3792-0.06220.0685-0.01420.01790.15930.00230.108727.7703-6.4015-7.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 201
2X-RAY DIFFRACTION2B20 - 201
3X-RAY DIFFRACTION3C16 - 151

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