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- PDB-7shh: Bacterial cereblon homologue in complex with (R)-3-(4-methoxyphen... -

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Basic information

Entry
Database: PDB / ID: 7shh
TitleBacterial cereblon homologue in complex with (R)-3-(4-methoxyphenyl)piperidine-2,6-dione
ComponentsCereblon isoform 4
KeywordsSIGNALING PROTEIN / Cereblon / PROTAC / targeted protein degradation / TBD
Function / homologyCULT domain / CULT domain profile. / metal ion binding / (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione / Cereblon isoform 4
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsNithianantham, S. / Fischer, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Development of Potent and Selective Janus Kinase 2/3 Directing PG-PROTACs.
Authors: Alcock, L.J. / Chang, Y. / Jarusiewicz, J.A. / Actis, M. / Nithianantham, S. / Mayasundari, A. / Min, J. / Maxwell, D. / Hunt, J. / Smart, B. / Yang, J.J. / Nishiguchi, G. / Fischer, M. / ...Authors: Alcock, L.J. / Chang, Y. / Jarusiewicz, J.A. / Actis, M. / Nithianantham, S. / Mayasundari, A. / Min, J. / Maxwell, D. / Hunt, J. / Smart, B. / Yang, J.J. / Nishiguchi, G. / Fischer, M. / Mullighan, C.G. / Rankovic, Z.
History
DepositionOct 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9239
Polymers41,0693
Non-polymers8546
Water1,26170
1
A: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9743
Polymers13,6901
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9743
Polymers13,6901
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cereblon isoform 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9743
Polymers13,6901
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.311, 59.586, 87.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 19 through 28 or resid 30...
21(chain B and (resid 19 through 28 or resid 30...
31(chain C and (resid 19 through 28 or resid 30...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLY(chain A and (resid 19 through 28 or resid 30...AA19 - 2820 - 29
12THRTHRSERSER(chain A and (resid 19 through 28 or resid 30...AA30 - 3231 - 33
13ARGARGARGARG(chain A and (resid 19 through 28 or resid 30...AA3334
14GLYGLYALAALA(chain A and (resid 19 through 28 or resid 30...AA18 - 12319 - 124
15GLYGLYALAALA(chain A and (resid 19 through 28 or resid 30...AA18 - 12319 - 124
16GLYGLYALAALA(chain A and (resid 19 through 28 or resid 30...AA18 - 12319 - 124
17GLYGLYALAALA(chain A and (resid 19 through 28 or resid 30...AA18 - 12319 - 124
21ALAALAGLYGLY(chain B and (resid 19 through 28 or resid 30...BB19 - 2820 - 29
22THRTHRSERSER(chain B and (resid 19 through 28 or resid 30...BB30 - 3231 - 33
23ARGARGARGARG(chain B and (resid 19 through 28 or resid 30...BB3334
24ALAALAALAALA(chain B and (resid 19 through 28 or resid 30...BB19 - 12320 - 124
25ALAALAALAALA(chain B and (resid 19 through 28 or resid 30...BB19 - 12320 - 124
26ALAALAALAALA(chain B and (resid 19 through 28 or resid 30...BB19 - 12320 - 124
27ALAALAALAALA(chain B and (resid 19 through 28 or resid 30...BB19 - 12320 - 124
31ALAALAGLYGLY(chain C and (resid 19 through 28 or resid 30...CC19 - 2820 - 29
32THRTHRLEULEU(chain C and (resid 19 through 28 or resid 30...CC30 - 3831 - 39
33METMETGLYGLY(chain C and (resid 19 through 28 or resid 30...CC40 - 5341 - 54
34PHEPHEPHEPHE(chain C and (resid 19 through 28 or resid 30...CC56 - 6157 - 62
35LEULEULEULEU(chain C and (resid 19 through 28 or resid 30...CC63 - 6764 - 68
36LEULEULEULEU(chain C and (resid 19 through 28 or resid 30...CC6970
37GLYGLYTRPTRP(chain C and (resid 19 through 28 or resid 30...CC71 - 8572 - 86
38ILEILEGLNGLN(chain C and (resid 19 through 28 or resid 30...CC87 - 10888 - 109
39PHEPHEALAALA(chain C and (resid 19 through 28 or resid 30...CC110 - 123111 - 124
310ZNZNZNZN(chain C and (resid 19 through 28 or resid 30...CH201

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Components

#1: Protein Cereblon isoform 4


Mass: 13689.552 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: MGR_0879 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-9FT / (3R)-3-(4-methoxyphenyl)piperidine-2,6-dione


Mass: 219.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.79 Å3/Da / Density % sol: 31.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0. 1M sodium acetate and 16% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→56.31 Å / Num. obs: 23597 / % possible obs: 98.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Net I/σ(I): 16.2 / Num. measured all: 311502 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9414.11.1042076014760.8430.3021.1452.698.3
9.11-56.3110.40.04727722660.9990.0140.04941.999.3

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
PHENIX1.12_2829phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→49.287 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1242 5.27 %
Rwork0.1915 22313 -
obs0.1927 23555 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.53 Å2 / Biso mean: 52.6615 Å2 / Biso min: 23.25 Å2
Refinement stepCycle: final / Resolution: 1.9→49.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 51 70 2498
Biso mean--50.38 49.72 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052594
X-RAY DIFFRACTIONf_angle_d0.8073536
X-RAY DIFFRACTIONf_chiral_restr0.054349
X-RAY DIFFRACTIONf_plane_restr0.006459
X-RAY DIFFRACTIONf_dihedral_angle_d3.5041914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1104X-RAY DIFFRACTION11.671TORSIONAL
12B1104X-RAY DIFFRACTION11.671TORSIONAL
13C1104X-RAY DIFFRACTION11.671TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.97610.2691220.2594242598
1.9761-2.0660.27891590.2369240798
2.066-2.1750.27611320.2168246699
2.175-2.31120.23841480.2114238997
2.3112-2.48970.23451250.1996249099
2.4897-2.74020.22321250.1976250199
2.7402-3.13670.22831490.1934250099
3.1367-3.95160.20851170.1724252399
3.9516-49.2870.1891650.1837261298
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)
16.19721.31221.19475.0178-0.80783.64810.03660.032-0.6636-0.13010.13680.10360.3214-0.4546-0.12140.2636-0.02740.00920.3199-0.0370.289916.592416.293610.0286
26.9644-0.8091-4.52232.24630.96515.2243-0.33460.3815-0.58480.17740.4126-0.61520.70040.8343-0.14420.31460.0701-0.04310.4892-0.17640.431225.768412.498-0.8918
34.41751.06031.14293.41090.4623.69780.00930.453-0.215-0.39430.04350.243-0.1222-0.1187-0.03650.21740.0436-0.01560.288-0.0680.251618.07220.337-0.7859
46.97134.10472.87786.55551.37636.9836-0.17570.1929-0.1471-0.42620.0408-0.7701-0.19480.82010.10140.26010.00480.04290.29620.06450.297842.33144.548922.2108
52.0062-1.63222.80482.0081-2.0087.37380.34030.09010.2104-1.0686-0.10970.87560.339-0.9705-0.17430.4288-0.0322-0.09610.3455-0.030.425227.78943.133414.2092
64.3371-3.9629-2.86699.78585.99489.4077-0.13020.02670.23080.60320.1958-0.07940.04520.3666-0.00880.22710.0021-0.00960.16650.04680.215424.893517.458120.0658
72.3446-1.19610.69052.2218-0.68542.0474-0.0054-0.2769-0.06580.31240.03230.3086-0.0869-0.1186-0.05370.3-0.01160.0510.21130.02830.293827.65688.021225.9722
84.8119-1.2272.22651.39050.14172.9667-0.1512-0.2689-0.3540.38480.12480.1383-0.1352-0.03350.050.2979-0.00150.04930.20350.05080.253631.42249.217430.2075
96.93931.5904-2.24333.8112-0.82434.7353-0.31470.2286-0.3987-0.27380.0969-0.04290.1469-0.11040.20770.27490.01260.0180.21060.01830.258832.89294.93322.0311
103.4362-1.94043.68132.6675-2.77736.89720.3539-0.0668-0.5005-0.0050.12060.5163-0.88760.2998-0.46090.4889-0.0191-0.00730.9823-0.29190.755928.95135.4308-9.5839
119.0307-0.15182.04516.60730.23626.0710.36920.51240.3574-0.0987-0.53390.9989-0.0616-0.61590.25730.4798-0.0093-0.02270.4835-0.13550.630531.90891.8134-9.0673
124.8144-1.4282-2.31232.03942.27641.5789-0.38870.6792-0.61281.44560.9880.90750.9345-0.4227-0.58151.0862-0.14040.00830.71980.11191.27918.5937-9.0567-5.2641
136.68340.5958-3.57824.8936-0.46136.7851-0.5173-0.8596-0.4043-0.53520.1692-0.4411-0.29930.04670.30590.7742-0.36150.02761.1824-0.13090.927921.4921-5.2866-5.2225
142.029-2.3221.99418.6276-2.2622.0204-0.04380.12050.54310.3634-0.9677-0.00011.0787-0.11250.88630.609-0.14860.13480.6457-0.08960.706836.2964-7.0436-9.1267
150.8721-0.0191-0.36031.8539-0.06573.29780.21170.201-0.1552-0.35640.7458-0.23-0.45270.1909-0.83761.3573-0.29460.04110.9411-0.02681.180425.5578-18.3178-6.014
164.69311.18530.10625.5857-0.15183.50050.36290.0615-1.06760.4505-0.53120.72941.5305-0.99920.14860.8392-0.25290.1220.7165-0.16520.862831.6555-11.586-6.7754
173.0726-0.78831.09247.68040.05972.3528-0.15130.0674-0.63140.0553-0.23540.6704-0.252-1.16260.48570.67-0.00420.13560.7599-0.23160.809627.43-1.1728-6.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 44 )A18 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 61 )A45 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 123 )A62 - 123
4X-RAY DIFFRACTION4chain 'B' and (resid 19 through 36 )B19 - 36
5X-RAY DIFFRACTION5chain 'B' and (resid 37 through 44 )B37 - 44
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 54 )B45 - 54
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 83 )B55 - 83
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 102 )B84 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 123 )B103 - 123
10X-RAY DIFFRACTION10chain 'C' and (resid 18 through 24 )C18 - 24
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 36 )C25 - 36
12X-RAY DIFFRACTION12chain 'C' and (resid 37 through 54 )C37 - 54
13X-RAY DIFFRACTION13chain 'C' and (resid 55 through 61 )C55 - 61
14X-RAY DIFFRACTION14chain 'C' and (resid 62 through 70 )C62 - 70
15X-RAY DIFFRACTION15chain 'C' and (resid 71 through 83 )C71 - 83
16X-RAY DIFFRACTION16chain 'C' and (resid 84 through 109 )C84 - 109
17X-RAY DIFFRACTION17chain 'C' and (resid 110 through 123 )C110 - 123

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