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- PDB-8rq1: Crystal structure of CRBN-midi -

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Basic information

Entry
Database: PDB / ID: 8rq1
TitleCrystal structure of CRBN-midi
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 / transmembrane transporter binding / Potential therapeutics for SARS / 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 / transmembrane transporter binding / Potential therapeutics for SARS / protein ubiquitination / perinuclear region of cytoplasm / membrane / nucleus / metal ion binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsKroupova, 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
DepositionJan 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5442
Polymers37,4791
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.031, 96.405, 148.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Protein cereblon


Mass: 37478.805 Da / Num. of mol.: 1
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium citrate, 20% (w/v) PEG 3350, and 0.1 M BIS-TRIS propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→74.04 Å / Num. obs: 6975 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 88.9 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.41 / Net I/σ(I): 5
Reflection shellResolution: 3.11→3.16 Å / Redundancy: 11.6 % / Rmerge(I) obs: 6.797 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 688 / CC1/2: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→74.04 Å / SU ML: 0.5138 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2997 359 5.15 %
Rwork0.2667 6616 -
obs0.2684 6975 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.15 Å2
Refinement stepCycle: LAST / Resolution: 3.11→74.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 1 0 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342161
X-RAY DIFFRACTIONf_angle_d0.60462954
X-RAY DIFFRACTIONf_chiral_restr0.0419353
X-RAY DIFFRACTIONf_plane_restr0.0044378
X-RAY DIFFRACTIONf_dihedral_angle_d12.9669740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.560.36361120.35442143X-RAY DIFFRACTION98.86
3.56-4.480.32641220.28242182X-RAY DIFFRACTION99.78
4.48-74.040.26921250.23562291X-RAY DIFFRACTION99.88

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