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- PDB-6r1k: Cereblon isoform 4 from Magnetospirillum gryphiswaldense in compl... -

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Basic information

Entry
Database: PDB / ID: 6r1k
TitleCereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with compound 7c
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / proteolysis targeting chimera / PROTAC / protein degradation
Function / homologyCULT domain / CULT domain profile. / metal ion binding / Chem-JPB / PHOSPHATE ION / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense MSR-1 (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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)42,68811
Polymers41,1113
Non-polymers1,5778
Water2,216123
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1864
Polymers13,7041
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4124
Polymers13,7041
Non-polymers7083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0913
Polymers13,7041
Non-polymers3872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.230, 60.080, 88.520
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: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA20 - 12221 - 123
21PROPROBB20 - 12221 - 123
12ALAALAAA20 - 12321 - 124
22ALAALACC20 - 12321 - 124
13PROPROBB20 - 12221 - 123
23PROPROCC20 - 12221 - 123

NCS ensembles :
ID
1
2
3

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Components

#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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-JPB / ~{N}-[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]-2,4,6-tris(chloranyl)benzamide


Mass: 321.544 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H7Cl3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1.82 Å3/Da / Density % sol: 32.36 %
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: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→47.46 Å / Num. obs: 26327 / % possible obs: 99.8 % / Redundancy: 12.95 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.46
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 13 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 4142 / CC1/2: 0.86 / % possible all: 98.9

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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: 1.94→47.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.136 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21222 1135 5 %RANDOM
Rwork0.17518 ---
obs0.17704 21565 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.107 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--1.93 Å2-0 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.94→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 84 123 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192651
X-RAY DIFFRACTIONr_bond_other_d0.0020.022284
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9023595
X-RAY DIFFRACTIONr_angle_other_deg1.0522.9895256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86821.452124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01615377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6421521
X-RAY DIFFRACTIONr_chiral_restr0.1110.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023021
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
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_it2.0873.291257
X-RAY DIFFRACTIONr_mcbond_other2.0873.2881256
X-RAY DIFFRACTIONr_mcangle_it3.1254.9131568
X-RAY DIFFRACTIONr_mcangle_other3.1254.9151569
X-RAY DIFFRACTIONr_scbond_it2.93.7221394
X-RAY DIFFRACTIONr_scbond_other2.8873.7211394
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4995.4632024
X-RAY DIFFRACTIONr_long_range_B_refined6.60237.5972884
X-RAY DIFFRACTIONr_long_range_B_other6.58537.5122879
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)
11A61780.12
12B61780.12
21A60180.11
22C60180.11
31B60020.12
32C60020.12
LS refinement shellResolution: 1.942→1.992 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 79 -
Rwork0.218 1502 -
obs--96.58 %
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)
11.3668-0.04480.81921.65360.44923.36830.09960.1821-0.1149-0.048-0.02660.00710.06770.0169-0.0730.02690.0308-0.02770.093-0.05260.10318.905517.92981.8729
21.8082-1.05080.22392.2-0.29962.0652-0.04080.0307-0.10890.036-0.01890.0971-0.11650.03580.05970.053-0.0230.0170.01680.00250.037531.36187.453123.9689
31.78751.0201-0.79592.58-0.39043.19450.019-0.0892-0.2005-0.08070.01720.24510.3259-0.5197-0.03620.0586-0.0861-0.01220.14880.01210.141327.6205-6.856-7.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 123
2X-RAY DIFFRACTION2B19 - 123
3X-RAY DIFFRACTION3C20 - 151

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