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

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Basic information

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

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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)41,9929
Polymers41,1113
Non-polymers8816
Water2,270126
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9973
Polymers13,7041
Non-polymers2942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9973
Polymers13,7041
Non-polymers2942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9973
Polymers13,7041
Non-polymers2942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.052, 59.905, 88.518
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-A1IW6 / (3~{S})-3-indol-1-ylpiperidine-2,6-dione


Mass: 228.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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

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 S 16M / Detector: PIXEL / Date: Feb 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 26222 / % possible obs: 99.7 % / Redundancy: 13.01 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.01
Reflection shellResolution: 1.85→1.96 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 4091 / CC1/2: 0.616

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→19.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.476 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24006 1315 5 %RANDOM
Rwork0.19634 ---
obs0.19849 24906 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.335 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å20 Å2
2--1.63 Å20 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 54 126 2576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132620
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182273
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.6413570
X-RAY DIFFRACTIONr_angle_other_deg1.4161.5745193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52719.774133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4311520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
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_it0.911.3271292
X-RAY DIFFRACTIONr_mcbond_other0.9091.3271291
X-RAY DIFFRACTIONr_mcangle_it1.5041.9781620
X-RAY DIFFRACTIONr_mcangle_other1.5041.9781621
X-RAY DIFFRACTIONr_scbond_it1.1851.4511328
X-RAY DIFFRACTIONr_scbond_other1.1851.4511329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.932.1291948
X-RAY DIFFRACTIONr_long_range_B_refined4.99815.4972885
X-RAY DIFFRACTIONr_long_range_B_other4.96415.2772872
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 / Rms dev position: 0.13 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A3080
12B3080
21A2896
22C2896
31B2699
32C2699
LS refinement shellResolution: 1.85→1.893 Å
RfactorNum. reflection% reflection
Rfree0.465 96 -
Rwork0.448 1749 -
obs--96.8 %
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)
13.1098-0.3370.34962.170.68673.86960.0790.0606-0.3942-0.0496-0.06590.15280.2733-0.0556-0.0130.19430.0093-0.02410.0165-0.02440.070119.057317.88052.7437
23.5832-1.32190.61142.9555-0.21762.79-0.0043-0.0924-0.1908-0.04620.05370.11740.03860.0626-0.04930.188-0.01250.00540.00580.00440.011431.83287.714323.948
33.9161.70970.35974.3305-0.15241.6165-0.0323-0.0009-0.0945-0.17090.12580.37130.1363-0.3737-0.09350.3188-0.01540.01820.22570.0380.128827.9162-6.4682-6.8955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C17 - 201

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