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- PDB-6r0u: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r0u
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 5a and hydrolysis product
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation / hydrolysis product
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JO5 / Chem-JO8 / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHeim, C. / Hartmann, M.D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives.
Authors: Heim, C. / Pliatsika, D. / Mousavizadeh, F. / Bar, K. / Hernandez Alvarez, B. / Giannis, A. / Hartmann, M.D.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)42,45714
Polymers41,1113
Non-polymers1,34711
Water3,315184
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1585
Polymers13,7041
Non-polymers4544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1775
Polymers13,7041
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1234
Polymers13,7041
Non-polymers4203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.952, 59.583, 89.053
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-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA19 - 12220 - 123
21ALAALABB19 - 12220 - 123
12GLYGLYAA18 - 12219 - 123
22GLYGLYCC18 - 12219 - 123
13ALAALABB19 - 12220 - 123
23ALAALACC19 - 12220 - 123

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#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 MSR-1 (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli (E. coli) / References: UniProt: A4TVL0

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Non-polymers , 7 types, 195 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EF2 / S-Thalidomide


Mass: 258.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-JO8 / 3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid


Mass: 277.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-JO5 / 4-azanyl-2-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]isoindole-1,3-dione


Mass: 259.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9N3O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.4 M 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 PILATUS 6M-F / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.98 Å / Num. obs: 33924 / % possible obs: 99 % / Redundancy: 12.34 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.22
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 12.75 % / Rmerge(I) obs: 0.95 / Num. unique obs: 5368 / CC1/2: 0.88 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2Y

4v2y


Resolution: 1.7→47.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.264 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22674 1688 5 %RANDOM
Rwork0.18694 ---
obs0.18892 32233 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.033 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0 Å2
2--1.94 Å2-0 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 78 185 2744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192680
X-RAY DIFFRACTIONr_bond_other_d0.0030.022306
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9363642
X-RAY DIFFRACTIONr_angle_other_deg1.0793.0015314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5922.185119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83915378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7131519
X-RAY DIFFRACTIONr_chiral_restr0.1290.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213047
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
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_it2.0652.5531289
X-RAY DIFFRACTIONr_mcbond_other2.0652.5511288
X-RAY DIFFRACTIONr_mcangle_it3.1093.8111609
X-RAY DIFFRACTIONr_mcangle_other3.1083.8131610
X-RAY DIFFRACTIONr_scbond_it2.4552.8761391
X-RAY DIFFRACTIONr_scbond_other2.4512.8631387
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8494.192022
X-RAY DIFFRACTIONr_long_range_B_refined6.57429.9672997
X-RAY DIFFRACTIONr_long_range_B_other6.54329.732976
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)
11A60420.13
12B60420.13
21A58060.14
22C58060.14
31B57040.16
32C57040.16
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 112 -
Rwork0.334 2293 -
obs--95.93 %
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)
11.39470.17171.08881.36360.28013.2710.10670.0471-0.14880.045-0.00990.12270.07060.0168-0.09680.01130.0151-0.01510.0657-0.04260.05219.150717.62752.6723
21.5332-0.968-0.18992.0851-0.25421.93470.0491-0.05260.0008-0.0969-0.01670.0117-0.06210.124-0.03240.0642-0.02990.02390.0370.00210.024732.1387.484323.9144
32.18510.75590.66491.3548-0.04441.99360.1146-0.2583-0.2436-0.06960.09570.03130.3096-0.2578-0.21030.0642-0.0582-0.04180.08660.04680.058327.7132-6.365-6.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 161
2X-RAY DIFFRACTION2B19 - 161
3X-RAY DIFFRACTION3C18 - 160

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