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- PDB-9gjq: Crystal structure of humanised cereblon from Magnetospirillum gry... -

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Basic information

Entry
Database: PDB / ID: 9gjq
TitleCrystal structure of humanised cereblon from Magnetospirillum gryphiswaldense bound by dihydrouracil-indole compound [1-(1H-indol-6-yl)dihydro-2,4(1H,3H)-pyrimidinedione].
ComponentsCereblon isoform 4
KeywordsLIGASE / Cereblon / crbn / inhibitor / dihydrouracil
Function / homologyCULT domain / CULT domain profile. / metal ion binding / : / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.393 Å
AuthorsCollie, G.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of dihydrouracil cereblon binders
Authors: Michaelides, I.
History
DepositionAug 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3383
Polymers12,0441
Non-polymers2952
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.782, 82.305, 52.445
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

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Components

#1: Protein Cereblon isoform 4


Mass: 12043.549 Da / Num. of mol.: 1 / Mutation: A52H, M54Y, F56H, F77H, Y101F, R117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0
#2: Chemical ChemComp-A1IMN / 1-(1H-indol-6-yl)-1,3-diazinane-2,4-dione / 1-(1H-indol-6-yl)dihydro-2,4(1H,3H)-pyrimidinedione


Mass: 229.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % PEG8000, 8 % ethylene glycol and 100 mM Na-HEPES buffer (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9538 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 1.393→43.829 Å / Num. obs: 18772 / % possible obs: 94.2 % / Redundancy: 7.5 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 1.393→1.467 Å / Num. unique obs: 939 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.393→43.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 997 -RANDOM
Rwork0.1999 ---
obs0.2004 18772 82.4 %-
Displacement parametersBiso mean: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.4398 Å20 Å20 Å2
2---0.7256 Å20 Å2
3---0.2859 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.393→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms836 0 18 116 970
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011898HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.071221HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d291SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes155HARMONIC5
X-RAY DIFFRACTIONt_it898HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion102SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact857SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.26
X-RAY DIFFRACTIONt_other_torsion15.04
LS refinement shellResolution: 1.393→1.43 Å
RfactorNum. reflection% reflection
Rfree0.3093 24 -
Rwork0.2566 --
obs--20.46 %

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