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

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Basic information

Entry
Database: PDB / ID: 9htp
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2p
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: 2.35 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)41,5257
Polymers41,1113
Non-polymers4144
Water21612
1
A: 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
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9873
Polymers13,7041
Non-polymers2842
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)55.831, 59.800, 86.868
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-A1IW5 / (3~{S})-3-[methyl(phenyl)amino]piperidine-2,6-dione


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.76 Å3/Da / Density % sol: 30.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4-0.6 M (NH4)H2PO4, ~17 mg/ml MSCI4 with 3mM 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 X CdTe 16M / Detector: PIXEL / Date: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 23376 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 59.56 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.132 / Net I/σ(I): 9.51
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3748 / CC1/2: 0.481 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→49.26 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 28.792 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28066 627 5 %RANDOM
Rwork0.23838 ---
obs0.24044 11989 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.364 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-0 Å2-0 Å2
2---4.84 Å20 Å2
3---7.83 Å2
Refinement stepCycle: 1 / Resolution: 2.35→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 19 12 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132323
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181974
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6373151
X-RAY DIFFRACTIONr_angle_other_deg1.2341.584499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11220120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77215288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6931517
X-RAY DIFFRACTIONr_chiral_restr0.0540.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022739
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
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_it1.0193.3651174
X-RAY DIFFRACTIONr_mcbond_other1.0193.3651173
X-RAY DIFFRACTIONr_mcangle_it1.7165.041458
X-RAY DIFFRACTIONr_mcangle_other1.7155.041459
X-RAY DIFFRACTIONr_scbond_it1.0253.4161149
X-RAY DIFFRACTIONr_scbond_other1.0243.4161150
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7095.0991692
X-RAY DIFFRACTIONr_long_range_B_refined3.31337.3562521
X-RAY DIFFRACTIONr_long_range_B_other3.31237.3622522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2991 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 40 -
Rwork0.397 858 -
obs--99.78 %
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)
13.31230.8261.65643.35161.48564.3472-0.01850.1058-0.2055-0.0653-0.01670.19550.3894-0.09830.03530.28320.0224-0.00280.2842-0.02460.033719.043718.52632.2635
23.3515-1.38320.65954.4966-0.93032.46810.03810.0186-0.24150.0165-0.0546-0.02930.01020.1510.01650.2675-0.0270.00510.26210.04060.028731.89498.498623.7388
31.80641.36370.6643.1149-0.3033.16670.12140.0681-0.1582-0.0043-0.10750.70380.0705-0.4747-0.01390.4985-0.01540.09430.5757-0.08130.444229.1846-5.6153-7.1449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 150
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C17 - 150

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