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- PDB-9gao: Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopipe... -

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Basic information

Entry
Database: PDB / ID: 9gao
TitleCrystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide
ComponentsProtein cereblon
KeywordsLIGASE / E3 ligase / PROTAC / TPD / molecular glue / targeted protein degradation
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination ...negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination / perinuclear region of cytoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily
Similarity search - Domain/homology
: / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRutter, Z.J. / Kroupova, A. / Zollman, D. / Ciulli, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2024
Title: Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders.
Authors: Kroupova, A. / Spiteri, V.A. / Rutter, Z.J. / Furihata, H. / Darren, D. / Ramachandran, S. / Chakraborti, S. / Haubrich, K. / Pethe, J. / Gonzales, D. / Wijaya, A.J. / Rodriguez-Rios, M. / ...Authors: Kroupova, A. / Spiteri, V.A. / Rutter, Z.J. / Furihata, H. / Darren, D. / Ramachandran, S. / Chakraborti, S. / Haubrich, K. / Pethe, J. / Gonzales, D. / Wijaya, A.J. / Rodriguez-Rios, M. / Sturbaut, M. / Lynch, D.M. / Farnaby, W. / Nakasone, M.A. / Zollman, D. / Ciulli, A.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Advisory / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein cereblon
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6416
Polymers74,9582
Non-polymers6834
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-13 kcal/mol
Surface area26000 Å2
Unit cell
Length a, b, c (Å)53.507, 94.862, 147.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein cereblon


Mass: 37478.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Chemical ChemComp-A1IJM / 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide


Mass: 276.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Buffer system I (Molecular Dimensions), 15.45% v/v Precipitant mix 2 (MD), 180 mM Monosaccharides (MD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.948→79.857 Å / Num. obs: 55330 / % possible obs: 98.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 38.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.7
Reflection shellResolution: 1.948→1.982 Å / Num. unique obs: 2794 / CC1/2: 0.293

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158-000refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→73.98 Å / SU ML: 0.3243 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2863 2694 4.98 %
Rwork0.252 51438 -
obs0.2537 54132 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.21 Å2
Refinement stepCycle: LAST / Resolution: 1.95→73.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 42 107 5084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345083
X-RAY DIFFRACTIONf_angle_d0.69836912
X-RAY DIFFRACTIONf_chiral_restr0.0468792
X-RAY DIFFRACTIONf_plane_restr0.0057887
X-RAY DIFFRACTIONf_dihedral_angle_d13.9621689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.4161130.42072034X-RAY DIFFRACTION73.33
1.98-2.020.43431290.39612717X-RAY DIFFRACTION98.72
2.02-2.060.43191570.37262664X-RAY DIFFRACTION97.21
2.06-2.110.37651190.35652559X-RAY DIFFRACTION92.89
2.11-2.160.34281380.31682759X-RAY DIFFRACTION99.83
2.16-2.210.34341420.30172777X-RAY DIFFRACTION99.93
2.21-2.270.34221360.30242757X-RAY DIFFRACTION99.28
2.27-2.340.31881580.29882738X-RAY DIFFRACTION99.76
2.34-2.410.31111510.27992767X-RAY DIFFRACTION99.79
2.41-2.50.31591390.27552746X-RAY DIFFRACTION99.79
2.5-2.60.34551380.28842799X-RAY DIFFRACTION99.9
2.6-2.720.35581300.29122674X-RAY DIFFRACTION95.8
2.72-2.860.28611410.27042818X-RAY DIFFRACTION99.93
2.86-3.040.31321530.28392781X-RAY DIFFRACTION99.97
3.04-3.280.31331580.28082783X-RAY DIFFRACTION99.97
3.28-3.610.28991460.25012695X-RAY DIFFRACTION95.43
3.61-4.130.28011290.2252527X-RAY DIFFRACTION88.74
4.13-5.20.21211520.18712858X-RAY DIFFRACTION99.93
5.2-73.980.23881650.20672985X-RAY DIFFRACTION99.15

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