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- PDB-8aop: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 8aop
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 14r
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / PROTEOLYSIS TARGETING CHIMERA / PROTAC / PROTEIN DEGRADATION
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-MW6 / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.944 Å
AuthorsMaiwald, S. / Heim, C. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Synthesis of novel glutarimide ligands for the E3 ligase substrate receptor Cereblon (CRBN): Investigation of their binding mode and antiproliferative effects against myeloma cell lines.
Authors: Krasavin, M. / Adamchik, M. / Bubyrev, A. / Heim, C. / Maiwald, S. / Zhukovsky, D. / Zhmurov, P. / Bunev, A. / Hartmann, M.D.
History
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)41,78410
Polymers40,8983
Non-polymers8877
Water1,02757
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0434
Polymers13,6331
Non-polymers4113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0434
Polymers13,6331
Non-polymers4113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6982
Polymers13,6331
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.790, 59.194, 87.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 20 - 122 / Label seq-ID: 20 - 122

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Cereblon isoform 4 / CULT domain-containing protein


Mass: 13632.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / 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-MW6 / (3S)-3-[(3-aminophenyl)sulfanylmethyl]piperidine-2,6-dione


Mass: 250.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 294 K / Method: vapor diffusion, sitting drop / Details: 0.4M Ammonium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→47.7 Å / Num. obs: 22417 / % possible obs: 100 % / Redundancy: 6.93 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.51
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6778 / CC1/2: 0.733 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4v2y

4v2y


Resolution: 1.944→47.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.009 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2272 1119 4.992 %
Rwork0.1967 21298 -
all0.198 --
obs-22417 99.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 52.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.283 Å2-0 Å2-0 Å2
2--1.195 Å2-0 Å2
3----1.478 Å2
Refinement stepCycle: LAST / Resolution: 1.944→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 47 57 2121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132137
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181917
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6382880
X-RAY DIFFRACTIONr_angle_other_deg1.2321.584389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6775258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33520.541111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7771516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
X-RAY DIFFRACTIONr_nbd_refined0.1750.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21634
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2969
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.224
X-RAY DIFFRACTIONr_nbd_other0.2210.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.214
X-RAY DIFFRACTIONr_mcbond_it1.4123.5271044
X-RAY DIFFRACTIONr_mcbond_other1.4133.5271043
X-RAY DIFFRACTIONr_mcangle_it2.1955.2751295
X-RAY DIFFRACTIONr_mcangle_other2.1945.2751296
X-RAY DIFFRACTIONr_scbond_it1.8453.7761093
X-RAY DIFFRACTIONr_scbond_other1.8453.7761094
X-RAY DIFFRACTIONr_scangle_it2.9185.5821584
X-RAY DIFFRACTIONr_scangle_other2.9175.5831585
X-RAY DIFFRACTIONr_lrange_it4.39838.7832213
X-RAY DIFFRACTIONr_lrange_other4.39738.7932214
X-RAY DIFFRACTIONr_ncsr_local_group_10.1090.053010
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.109310.05008
12BX-RAY DIFFRACTIONLocal ncs0.109310.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.944-1.9950.254790.2711551X-RAY DIFFRACTION99.6942
1.995-2.0490.235810.2411520X-RAY DIFFRACTION100
2.049-2.1090.27790.2141470X-RAY DIFFRACTION100
2.109-2.1730.258680.21412X-RAY DIFFRACTION100
2.173-2.2440.21780.2021357X-RAY DIFFRACTION100
2.244-2.3230.285660.2041350X-RAY DIFFRACTION100
2.323-2.4110.181670.181307X-RAY DIFFRACTION100
2.411-2.5090.255700.1941251X-RAY DIFFRACTION100
2.509-2.620.22620.1941194X-RAY DIFFRACTION100
2.62-2.7470.2590.1991160X-RAY DIFFRACTION100
2.747-2.8960.201590.1951078X-RAY DIFFRACTION100
2.896-3.0710.217540.1871055X-RAY DIFFRACTION100
3.071-3.2820.194510.187998X-RAY DIFFRACTION100
3.282-3.5430.219490.183915X-RAY DIFFRACTION100
3.543-3.8790.205460.18859X-RAY DIFFRACTION100
3.879-4.3340.172400.171763X-RAY DIFFRACTION100
4.334-4.9980.211370.174697X-RAY DIFFRACTION99.8639
4.998-6.1050.262320.224590X-RAY DIFFRACTION100
6.105-8.5680.327250.24476X-RAY DIFFRACTION100
8.568-47.70.36170.246295X-RAY DIFFRACTION98.7342
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)
13.15940.08761.86141.98751.66126.17480.05130.1348-0.20110.0007-0.03070.09270.17460.0186-0.02060.00920.0111-0.00970.0438-0.03260.111619.185417.7761.8547
23.1501-1.9338-0.28245.2546-1.20243.7675-0.0105-0.1992-0.03910.0976-0.0375-0.0631-0.03870.2540.0480.0268-0.01930.00690.04660.02410.077631.81688.105223.9187
35.9617-0.2071.7584.5070.19857.4537-0.04680.2203-0.5242-0.2836-0.12750.73960.3931-0.9550.17430.2548-0.09160.04720.498-0.15010.501431.85-1.3404-6.9129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA19 - 327
2X-RAY DIFFRACTION2ALLB20 - 329
3X-RAY DIFFRACTION3ALLC18 - 301

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