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- PDB-6r1a: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r1a
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 20b
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JP8 / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45913
Polymers41,1113
Non-polymers1,34810
Water4,179232
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)14,2175
Polymers13,7041
Non-polymers5144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1194
Polymers13,7041
Non-polymers4163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.556, 59.309, 88.004
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
11METMETAA13 - 12214 - 123
21METMETBB13 - 12214 - 123
12ALAALAAA16 - 12217 - 123
22ALAALACC16 - 12217 - 123
13ALAALABB16 - 12217 - 123
23ALAALACC16 - 12217 - 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 , 5 types, 242 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.: 2 / Source method: obtained synthetically / Formula: C13H10N2O4 / Comment: medication*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-JP8 / [(2~{R})-pyrrolidin-2-yl]methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate


Mass: 255.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 31.48 %
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: 1.54→49.18 Å / Num. obs: 44027 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.28
Reflection shellResolution: 1.54→1.64 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 6798 / CC1/2: 0.84 / % possible all: 96.7

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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: 1.54→49.18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.904 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20809 2201 5 %RANDOM
Rwork0.17974 ---
obs0.18114 41826 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0 Å2
2--0.53 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.54→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 79 232 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192803
X-RAY DIFFRACTIONr_bond_other_d0.0030.022444
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9513817
X-RAY DIFFRACTIONr_angle_other_deg1.043.0045640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41422125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1051522
X-RAY DIFFRACTIONr_chiral_restr0.1110.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
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_it1.0741.7651343
X-RAY DIFFRACTIONr_mcbond_other1.0731.7651342
X-RAY DIFFRACTIONr_mcangle_it1.812.6361679
X-RAY DIFFRACTIONr_mcangle_other1.812.6361680
X-RAY DIFFRACTIONr_scbond_it1.391.9121460
X-RAY DIFFRACTIONr_scbond_other1.391.8961457
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2542.7922122
X-RAY DIFFRACTIONr_long_range_B_refined4.61720.5463152
X-RAY DIFFRACTIONr_long_range_B_other4.32920.3923143
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)
11A65000.14
12B65000.14
21A60280.17
22C60280.17
31B59120.19
32C59120.19
LS refinement shellResolution: 1.543→1.583 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 152 -
Rwork0.293 2816 -
obs--92.55 %
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)
10.6466-0.05430.47840.11180.12121.14330.046-0.0229-0.0303-0.00240.01020.02310.0194-0.0043-0.05620.0070.0048-0.00540.0661-0.02380.027218.807817.50153.0886
20.7925-0.4393-0.15740.455-0.27190.76950.0289-0.0266-0.0657-0.0379-0.03780.0443-0.01550.06460.0090.0275-0.0015-0.00270.05640.00730.024832.51376.655523.2348
31.85340.27661.30651.61091.36631.79510.1023-0.2582-0.26330.2542-0.08980.18570.2475-0.2245-0.01250.0421-0.02170.02240.13390.00160.086427.4162-6.212-6.7143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 391
2X-RAY DIFFRACTION2B13 - 397
3X-RAY DIFFRACTION3C16 - 344

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