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- PDB-6r0q: Mutant cereblon isoform 4 from Magnetospirillum gryphiswaldense i... -

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Basic information

Entry
Database: PDB / ID: 6r0q
TitleMutant cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with thalidomide metabolite alpha-(o-carboxybenzamido)glutarimide
Components
  • ALA-ALA-ALA
  • ALA-ALA-ALA-ALA
  • Cereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation / hydrolysis product
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-JNW / 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 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 / refine / 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 / _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
F: ALA-ALA-ALA
E: ALA-ALA-ALA
G: ALA-ALA-ALA
H: ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,61116
Polymers56,2448
Non-polymers1,3678
Water7,584421
1
A: Cereblon isoform 4
F: ALA-ALA-ALA
H: ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7405
Polymers14,3983
Non-polymers3422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1083
Polymers13,7661
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
E: ALA-ALA-ALA
G: ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6555
Polymers14,3133
Non-polymers3422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1083
Polymers13,7661
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.728, 59.163, 61.751
Angle α, β, γ (deg.)90.00, 105.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11SERSERPROPROAA20 - 12220 - 122
21SERSERPROPROBB20 - 12220 - 122
12GLYGLYASPASPAA18 - 12418 - 124
22GLYGLYASPASPCC18 - 12418 - 124
13SERSERPROPROAA20 - 12220 - 122
23SERSERPROPRODD20 - 12220 - 122
14SERSERPROPROBB20 - 12220 - 122
24SERSERPROPROCC20 - 12220 - 122
15SERSERALAALABB20 - 12320 - 123
25SERSERALAALADD20 - 12320 - 123
16SERSERPROPROCC20 - 12220 - 122
26SERSERPROPRODD20 - 12220 - 122

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cereblon isoform 4


Mass: 13766.490 Da / Num. of mol.: 4 / Mutation: A52H, M54Y, F56H, R68N, A72R, I87V, L89Q
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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Protein/peptide , 2 types, 4 molecules FEGH

#2: Protein/peptide ALA-ALA-ALA


Mass: 273.330 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense MSR-1 (magnetotactic)
Production host: Escherichia coli (E. coli)
#3: Protein/peptide ALA-ALA-ALA-ALA


Mass: 358.434 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 , 3 types, 429 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-JNW / 2-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamoyl]benzoic acid


Mass: 276.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H12N2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 1.94 Å3/Da / Density % sol: 36.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 3350, 0.2 M Ammonium acetate

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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: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→49.17 Å / Num. obs: 68423 / % possible obs: 99 % / Redundancy: 3.37 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.14 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 10911 / CC1/2: 0.56 / % possible all: 97.5

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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: 1.5→49.17 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.261 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19039 3422 5 %RANDOM
Rwork0.1578 ---
obs0.15943 65001 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.669 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.18 Å2
2--0.32 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 84 421 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0193706
X-RAY DIFFRACTIONr_bond_other_d0.0020.023107
X-RAY DIFFRACTIONr_angle_refined_deg4.4091.935021
X-RAY DIFFRACTIONr_angle_other_deg1.4073.0047157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60822.151186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42615521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131531
X-RAY DIFFRACTIONr_chiral_restr0.1980.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0430.024230
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02907
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_it2.6411.5881764
X-RAY DIFFRACTIONr_mcbond_other2.6351.5851763
X-RAY DIFFRACTIONr_mcangle_it3.8442.3342189
X-RAY DIFFRACTIONr_mcangle_other3.8442.3382190
X-RAY DIFFRACTIONr_scbond_it3.4071.8581942
X-RAY DIFFRACTIONr_scbond_other3.4061.8611943
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2642.6642822
X-RAY DIFFRACTIONr_long_range_B_refined7.24618.5864156
X-RAY DIFFRACTIONr_long_range_B_other7.22918.5894156
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)
11A60560.14
12B60560.14
21A67900.06
22C67900.06
31A62080.13
32D62080.13
41B61360.13
42C61360.13
51B65240.07
52D65240.07
61C63140.13
62D63140.13
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 244 -
Rwork0.386 4634 -
obs--96.46 %
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)
10.56780.11270.10480.40910.09280.43910.0190.0477-0.03990.0049-0.003-0.0155-0.01380.0311-0.0160.04060.0027-0.01080.0376-0.00980.0065-4.4616-0.07116.1884
20.3072-0.0517-0.21540.24290.02620.808-0.00610.0004-0.04130.0299-0.02730.0001-0.0837-0.07740.03340.04350.0118-0.0080.0420.00080.0078-17.15680.733136.8454
30.3872-0.06270.0670.3707-0.16340.620.0026-0.0194-0.01650.02250.00440.0043-0.0407-0.0518-0.0070.02820.0116-0.01580.03680.00210.012616.7655-2.47160.0205
40.8347-0.0254-0.08380.15120.08060.26310.04790.0651-0.06410.0058-0.0209-0.03-0.0270.0146-0.0270.02740.0015-0.0150.0398-0.00960.020440.0716-3.3215-6.5087
500000000000000-00.0339000.033900.0339000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 409
2X-RAY DIFFRACTION2B20 - 396
3X-RAY DIFFRACTION3C18 - 404
4X-RAY DIFFRACTION4D20 - 407

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