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

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Basic information

Entry
Database: PDB / ID: 9htl
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with glutarimide based compound 2j
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / CEREBLON / Ubiquitination / E3 / MOLECULAR GLUE
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: 1.74 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)41,8129
Polymers41,1113
Non-polymers7026
Water1,44180
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0694
Polymers13,7041
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9743
Polymers13,7041
Non-polymers2712
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)56.507, 59.361, 88.337
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-A1IW9 / (3~{R})-3-phenoxypiperidine-2,6-dione


Mass: 205.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO3 / 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.: 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: 1.78 Å3/Da / Density % sol: 30.99 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 58605 / % possible obs: 99.8 % / Redundancy: 6.96 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.31
Reflection shellResolution: 1.74→1.85 Å / Redundancy: 6.79 % / Mean I/σ(I) obs: 1.57 / Num. unique obs: 9397 / CC1/2: 0.611 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.74→47.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.393 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1556 5 %RANDOM
Rwork0.18387 ---
obs0.18549 29479 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.748 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--1.55 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.74→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 38 80 2520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132645
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182308
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6423605
X-RAY DIFFRACTIONr_angle_other_deg1.41.5755280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0335337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99619.701134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58915350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.411521
X-RAY DIFFRACTIONr_chiral_restr0.0750.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02723
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_it1.091.9831318
X-RAY DIFFRACTIONr_mcbond_other1.091.9831317
X-RAY DIFFRACTIONr_mcangle_it1.7582.9651656
X-RAY DIFFRACTIONr_mcangle_other1.7582.9651657
X-RAY DIFFRACTIONr_scbond_it1.6642.1551327
X-RAY DIFFRACTIONr_scbond_other1.6372.1511324
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5763.1651941
X-RAY DIFFRACTIONr_long_range_B_refined4.55222.3762828
X-RAY DIFFRACTIONr_long_range_B_other4.53722.3412826
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)
11A31640.13
12B31640.13
21A28170.13
22C28170.13
31B27340.14
32C27340.14
LS refinement shellResolution: 1.742→1.787 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 117 -
Rwork0.267 2103 -
obs--98.89 %
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)
12.30310.02751.12261.88051.20624.570.0570.0638-0.2276-0.0326-0.00970.09590.2693-0.011-0.04730.06840.0113-0.0110.0236-0.03810.139318.915617.69252.8136
23.3031-1.33850.15163.0128-0.27042.32420.0035-0.0626-0.1291-0.0528-0.00760.03340.01790.06310.00410.0692-0.00850.01020.00680.01430.082831.91877.490323.8212
33.61831.37760.94243.86050.10953.24280.0494-0.0905-0.1411-0.10390.01160.41080.2868-0.5748-0.0610.1787-0.04140.02780.2683-0.00250.252528.5342-6.0382-7.4331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 201
2X-RAY DIFFRACTION2B19 - 201
3X-RAY DIFFRACTION3C17 - 150

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