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

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Basic information

Entry
Database: PDB / ID: 9htm
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2o
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: 1.85 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

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)41,9209
Polymers41,1113
Non-polymers8096
Water1,44180
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9733
Polymers13,7041
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9733
Polymers13,7041
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9733
Polymers13,7041
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.299, 59.620, 88.446
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-A1IW8 / (3R)-3-phenylazanylpiperidine-2,6-dione


Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1I4P / (3S)-3-phenylazanylpiperidine-2,6-dione


Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.74 Å3/Da / Density % sol: 29.36 %
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: 1.85→50 Å / Num. obs: 26041 / % possible obs: 99.2 % / Redundancy: 12.92 % / Biso Wilson estimate: 39.26 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.12
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 13.06 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3960 / CC1/2: 0.518 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→47.54 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.253 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 1303 5 %RANDOM
Rwork0.18956 ---
obs0.19189 24738 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--1.11 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 1.85→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 48 80 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132663
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172314
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6393635
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5735293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2095342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70719.542131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2415343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3261520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
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_it1.2692.2411323
X-RAY DIFFRACTIONr_mcbond_other1.272.2411322
X-RAY DIFFRACTIONr_mcangle_it2.0193.3551665
X-RAY DIFFRACTIONr_mcangle_other2.0183.3551666
X-RAY DIFFRACTIONr_scbond_it1.6122.4091340
X-RAY DIFFRACTIONr_scbond_other1.6122.411341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5483.5531966
X-RAY DIFFRACTIONr_long_range_B_refined4.60625.3932860
X-RAY DIFFRACTIONr_long_range_B_other4.60425.3442857
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)
11A31140.13
12B31140.13
21A28530.14
22C28530.14
31B27140.14
32C27140.14
LS refinement shellResolution: 1.85→1.894 Å
RfactorNum. reflection% reflection
Rfree0.377 86 -
Rwork0.351 1594 -
obs--89.22 %
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)
12.8634-0.31690.42931.92691.12374.77220.07370.028-0.2601-0.0554-0.02250.11960.3217-0.0607-0.05120.0340.005-0.02250.0392-0.04580.127818.908317.7462.8607
23.6345-1.35410.64992.9387-0.15852.44670.0123-0.0504-0.1202-0.0573-0.01080.01920.01880.0715-0.00160.0042-0.00480.00310.02830.02290.064631.94987.568723.8224
33.87071.02731.05443.68440.2123.0160.0518-0.0645-0.1103-0.09190.07990.43760.1925-0.5682-0.13170.1274-0.02270.03690.33160.10620.24628.1477-6.4954-6.9736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C17 - 151

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