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

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Basic information

Entry
Database: PDB / ID: 8aoq
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20a
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / PROTEOLYSIS TARGETING CHIMERA / PROTAC / PROTEIN DEGRADATION
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-N8F / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.088 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)41,6288
Polymers40,8983
Non-polymers7315
Water81145
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9653
Polymers13,6331
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9653
Polymers13,6331
Non-polymers3332
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.660, 59.169, 88.334
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: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 19 - 123 / Label seq-ID: 19 - 123

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


Mass: 13632.500 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 (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-N8F / (3~{S})-3-(phenylsulfonylmethyl)piperidine-2,6-dione


Mass: 267.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.088→49.2 Å / Num. obs: 18215 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.04
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 6.96 % / Rmerge(I) obs: 0.857 / Mean I/σ(I) obs: 2 / Num. unique obs: 5523 / CC1/2: 0.784 / % 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: 2.088→49.16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.959 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2325 905 4.968 %
Rwork0.1945 17310 -
all0.196 --
obs-18215 99.929 %
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: 49.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.767 Å20 Å2-0 Å2
2--0.492 Å2-0 Å2
3----1.259 Å2
Refinement stepCycle: LAST / Resolution: 2.088→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 39 45 1969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132004
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181745
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6362712
X-RAY DIFFRACTIONr_angle_other_deg1.2631.5773983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1815248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90620.82597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82915262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2321512
X-RAY DIFFRACTIONr_chiral_restr0.060.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_nbd_refined0.1720.2334
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21550
X-RAY DIFFRACTIONr_nbtor_refined0.170.2910
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.261
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1310.221
X-RAY DIFFRACTIONr_nbd_other0.2110.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.26
X-RAY DIFFRACTIONr_mcbond_it1.5383.6811007
X-RAY DIFFRACTIONr_mcbond_other1.5393.681006
X-RAY DIFFRACTIONr_mcangle_it2.3885.5051250
X-RAY DIFFRACTIONr_mcangle_other2.3875.5061251
X-RAY DIFFRACTIONr_scbond_it1.953.851997
X-RAY DIFFRACTIONr_scbond_other1.9493.852998
X-RAY DIFFRACTIONr_scangle_it3.1165.6971462
X-RAY DIFFRACTIONr_scangle_other3.1155.6981463
X-RAY DIFFRACTIONr_lrange_it4.33341.0032105
X-RAY DIFFRACTIONr_lrange_other4.33241.0162106
X-RAY DIFFRACTIONr_ncsr_local_group_10.110.053029
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.109580.05008
12BX-RAY DIFFRACTIONLocal ncs0.109580.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.088-2.1420.253600.26812470.26713090.8920.89599.84720.251
2.142-2.2010.256660.22912230.2312890.9150.9141000.204
2.201-2.2650.22620.212080.20212700.9290.931000.173
2.265-2.3340.294560.22211520.22512080.9050.9271000.192
2.334-2.4110.234600.19811170.19911770.9320.9421000.165
2.411-2.4950.214560.18810900.18911460.9450.951000.16
2.495-2.5890.205570.18110690.18211260.9470.9551000.157
2.589-2.6940.235570.18510020.18810590.9420.9511000.155
2.694-2.8140.2510.1819780.18210300.9520.95299.90290.153
2.814-2.9510.214470.1819380.1829860.9520.95699.89860.158
2.951-3.110.227470.188900.1829370.9430.9561000.163
3.11-3.2970.218460.1878510.1898970.9410.9471000.176
3.297-3.5240.239410.1697990.1738400.9390.9521000.162
3.524-3.8050.203420.1817430.1827860.9450.95599.87280.178
3.805-4.1650.185340.1726890.1737230.9530.9621000.175
4.165-4.6530.202330.1526360.1556690.9620.9731000.163
4.653-5.3650.254300.185590.1835890.9430.9661000.199
5.365-6.5510.251270.2664870.2655140.9380.9291000.282
6.551-9.1830.308200.2583920.264120.9250.941000.294
9.183-49.160.409130.2792400.2842580.9290.93598.0620.36
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)
13.3063-0.13271.19322.53081.31816.28990.09320.1598-0.2913-0.0594-0.05880.15010.1707-0.0117-0.03440.01480.0149-0.02240.0295-0.03820.055519.13117.76892.1154
23.5886-2.3172-0.5315.5462-0.81163.5573-0.0235-0.1615-0.00610.08920.0039-0.1566-0.04380.28370.01960.0299-0.0103-0.00040.03030.00340.008932.04527.796123.8397
36.35911.48641.08284.0015-0.51725.0731-0.08280.1858-0.52020.0202-0.1150.80930.4114-0.80580.19770.3505-0.07760.05990.4798-0.15870.558832.76-0.4899-5.6637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA19 - 123
2X-RAY DIFFRACTION1ALLA201
3X-RAY DIFFRACTION1ALLA202
4X-RAY DIFFRACTION2ALLB19 - 123
5X-RAY DIFFRACTION2ALLB201
6X-RAY DIFFRACTION2ALLB202
7X-RAY DIFFRACTION3ALLC18 - 122

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