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- PDB-6r12: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r12
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7b
Components(Cereblon isoform ...) x 2
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation / hydrolysis product
Function / homologyCULT domain / CULT domain profile. / metal ion binding / S-Thalidomide / Chem-JOT / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
F: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,76014
Polymers41,5544
Non-polymers1,20610
Water3,423190
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
Buried area170 Å2
ΔGint-4 kcal/mol
Surface area5980 Å2
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1676
Polymers13,7041
Non-polymers4645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-17 kcal/mol
Surface area5810 Å2
MethodPISA
3
C: Cereblon isoform 4
hetero molecules

F: Cereblon isoform 4


Theoretical massNumber of molelcules
Total (without water)14,4714
Polymers14,1472
Non-polymers3242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area510 Å2
ΔGint-3 kcal/mol
Surface area5950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.417, 58.795, 88.234
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
11ALAALAPROPROAA19 - 12220 - 123
21ALAALAPROPROBB19 - 12220 - 123
12GLYGLYALAALAAA18 - 12319 - 124
22GLYGLYALAALACC18 - 12319 - 124
13ALAALAPROPROBB19 - 12220 - 123
23ALAALAPROPROCC19 - 12220 - 123

NCS ensembles :
ID
1
2
3

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Components

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

#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: 443.539 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, 200 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


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.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-JOT / ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2-phenyl-ethanamide


Mass: 232.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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

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: 1.73→48.93 Å / Num. obs: 30720 / % possible obs: 98.8 % / Redundancy: 12.46 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.55
Reflection shellResolution: 1.73→1.84 Å / Redundancy: 11.99 % / Rmerge(I) obs: 0.89 / Num. unique obs: 54861 / CC1/2: 0.86 / % possible all: 92.4

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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: 1.74→48.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.424 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 1530 5 %RANDOM
Rwork0.17405 ---
obs0.17703 29052 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.965 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0 Å2
2--1.95 Å2-0 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2505 0 70 190 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192688
X-RAY DIFFRACTIONr_bond_other_d0.0020.022316
X-RAY DIFFRACTIONr_angle_refined_deg2.2591.9113647
X-RAY DIFFRACTIONr_angle_other_deg1.2132.9855322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99421.613124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95715368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9441519
X-RAY DIFFRACTIONr_chiral_restr0.1740.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02661
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_it2.272.2891307
X-RAY DIFFRACTIONr_mcbond_other2.2662.2851306
X-RAY DIFFRACTIONr_mcangle_it3.3243.3971628
X-RAY DIFFRACTIONr_mcangle_other3.3263.4011629
X-RAY DIFFRACTIONr_scbond_it2.862.5091381
X-RAY DIFFRACTIONr_scbond_other2.8592.5121382
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2873.6622015
X-RAY DIFFRACTIONr_long_range_B_refined6.19125.732975
X-RAY DIFFRACTIONr_long_range_B_other6.17725.732975
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)
11A61900.13
12B61900.13
21A57320.16
22C57320.16
31B55940.17
32C55940.17
LS refinement shellResolution: 1.743→1.788 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 100 -
Rwork0.29 2059 -
obs--97.21 %
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)
11.79170.18981.56020.5710.37411.43820.04560.1477-0.0606-0.14340.0356-0.0558-0.01150.1422-0.08110.04520.0003-0.00520.0561-0.02910.087718.987717.35262.4385
20.5623-0.4209-0.0690.5539-0.37280.77130.0332-0.0392-0.0569-0.0197-0.0130.055-0.02850.0617-0.02020.0161-0.00410.00360.02880.0140.074231.65827.554223.7679
31.43120.12441.28862.14112.43163.68650.133-0.3219-0.43390.4166-0.14820.32130.5487-0.44430.01520.0921-0.02440.02620.25210.03940.199527.5731-6.3114-7.0566
400000000000000-00.0509000.050900.0509000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 376
2X-RAY DIFFRACTION2B19 - 378
3X-RAY DIFFRACTION3C18 - 335

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