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- PDB-6r18: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r18
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 11a
Components(Cereblon isoform ...) x 2
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JOQ / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.2Jan 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 / refine / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _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
D: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,69414
Polymers41,3844
Non-polymers1,31010
Water5,062281
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1224
Polymers13,7041
Non-polymers4193
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
D: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3965
Polymers13,9772
Non-polymers4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.630, 59.592, 88.894
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALALAALAAA14 - 12315 - 124
21VALVALALAALABB14 - 12315 - 124
12GLYGLYPROPROAA18 - 12219 - 123
22GLYGLYPROPROCC18 - 12219 - 123
13SERSERPROPROBB20 - 12221 - 123
23SERSERPROPROCC20 - 12221 - 123

NCS ensembles :
ID
1
2
3

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Components

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Cereblon isoform ... , 2 types, 4 molecules ABCD

#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
#2: Protein/peptide Cereblon isoform 4


Mass: 273.330 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 291 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 258.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-JOQ / [4-(aminomethyl)phenyl]methyl ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamate


Mass: 277.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H15N3O4
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 1.81 Å3/Da / Density % sol: 32.2 %
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: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→44.45 Å / Num. obs: 66849 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 17.62
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 10587 / CC1/2: 0.83 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v2y

4v2y


Resolution: 1.35→44.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.082 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19732 3318 5 %RANDOM
Rwork0.17287 ---
obs0.17409 63530 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å20 Å2
2--0.52 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 77 281 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192803
X-RAY DIFFRACTIONr_bond_other_d0.0020.022454
X-RAY DIFFRACTIONr_angle_refined_deg2.1481.9513815
X-RAY DIFFRACTIONr_angle_other_deg1.0663.0045661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59822.08125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.361521
X-RAY DIFFRACTIONr_chiral_restr0.1280.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213160
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02674
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_it1.411.5971337
X-RAY DIFFRACTIONr_mcbond_other1.411.5951336
X-RAY DIFFRACTIONr_mcangle_it2.2992.3791669
X-RAY DIFFRACTIONr_mcangle_other2.2992.3821670
X-RAY DIFFRACTIONr_scbond_it2.0281.8371466
X-RAY DIFFRACTIONr_scbond_other2.0231.8321463
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.182.6682127
X-RAY DIFFRACTIONr_long_range_B_refined5.21319.0813151
X-RAY DIFFRACTIONr_long_range_B_other5.20919.0783150
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)
11A63800.14
12B63800.14
21A59800.15
22C59800.15
31B58420.17
32C58420.17
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 224 -
Rwork0.312 4571 -
obs--98.38 %
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)
10.48510.0140.49170.12660.10331.04030.040.0037-0.03270.00890.01280.0236-0.0008-0.001-0.05280.01020.0094-0.0010.0495-0.01540.017718.86717.473.0314
20.5174-0.407-0.15140.4278-0.09640.49650.0125-0.0091-0.0371-0.0143-0.00790.0392-0.01420.0417-0.00460.0191-0.0105-0.00040.02780.00210.013232.39146.712623.5599
30.56990.34290.30190.5685-0.3991.11670.0087-0.0701-0.0349-0.04320.06940.01760.0581-0.1697-0.07810.0143-0.0250.00030.08810.01120.009327.6092-6.4071-7.0696
400000000000000-00.014000.01400.014000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 408
2X-RAY DIFFRACTION2B13 - 406
3X-RAY DIFFRACTION3C18 - 363

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