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- PDB-6r1c: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r1c
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 12a
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / ASPARTIC ACID / S-Thalidomide / Chem-JOW / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.1Jan 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)42,65414
Polymers41,1113
Non-polymers1,54411
Water3,999222
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2555
Polymers13,7041
Non-polymers5524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3726
Polymers13,7041
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0273
Polymers13,7041
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.656, 59.020, 88.593
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: _ / Refine code: _

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
13GLYGLYPROPROBB18 - 12219 - 123
23GLYGLYPROPROCC18 - 12219 - 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, 233 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#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


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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-JOW / 4-[[4-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyloxymethyl]phenyl]methylamino]-4-oxidanylidene-butanoic acid


Mass: 377.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N3O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.8 Å3/Da / Density % sol: 31.72 %
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: 1.5→49.12 Å / Num. obs: 48555 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.29
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 7572 / CC1/2: 0.87 / % possible all: 97.2

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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: 1.5→49.12 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.253 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21537 2427 5 %RANDOM
Rwork0.19354 ---
obs0.19463 46128 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0 Å2
2--0.78 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 93 222 2855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192784
X-RAY DIFFRACTIONr_bond_other_d0.0030.022415
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9363790
X-RAY DIFFRACTIONr_angle_other_deg1.0152.9925575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77221.953128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75515394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6511521
X-RAY DIFFRACTIONr_chiral_restr0.1060.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02675
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_it1.011.7571330
X-RAY DIFFRACTIONr_mcbond_other1.0091.7551329
X-RAY DIFFRACTIONr_mcangle_it1.7792.6171661
X-RAY DIFFRACTIONr_mcangle_other1.7792.6191662
X-RAY DIFFRACTIONr_scbond_it1.0851.891454
X-RAY DIFFRACTIONr_scbond_other1.0841.8911455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8252.8012119
X-RAY DIFFRACTIONr_long_range_B_refined4.83220.3223166
X-RAY DIFFRACTIONr_long_range_B_other4.8120.3063165
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)
11A65500.14
12B65500.14
21A60020.15
22C60020.15
31B58540.17
32C58540.17
LS refinement shellResolution: 1.495→1.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 167 -
Rwork0.374 3156 -
obs--93.79 %
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)
10.8233-0.06440.64590.18970.09171.1140.036-0.0192-0.04610.00570.02590.0281-0.0074-0.0066-0.06190.01810.0032-0.00620.057-0.01870.025918.777817.32013.1246
20.815-0.5558-0.15880.535-0.20550.78180.0264-0.0402-0.0581-0.0314-0.01740.0479-0.03520.0659-0.0090.0423-0.00560.00250.04150.0040.019832.616.856823.5141
31.51570.76281.28191.31450.26651.23910.0893-0.2737-0.05870.0197-0.00680.0280.092-0.2802-0.08250.0109-0.036-0.0010.15410.00630.011627.6804-6.1757-7.0911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 392
2X-RAY DIFFRACTION2B14 - 391
3X-RAY DIFFRACTION3C18 - 339

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