+Open data
-Basic information
Entry | Database: PDB / ID: 8rqa | ||||||
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Title | Crystal structure of CRBN-midi in complex with Lenalidomide | ||||||
Components | Protein cereblon | ||||||
Keywords | LIGASE / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rutter, Z.J. / Kroupova, A. / Zollman, D. / Ciulli, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders Authors: Kroupova, A. / Spiteri, V. / Furihata, H. / Darren, D. / Ramachandran, S. / Rutter, Z.J. / Chakraborti, S. / Haubrich, K. / Pethe, J. / Gonzales, D. / Wijaya, A. / Rodriguez-Rios, M. / ...Authors: Kroupova, A. / Spiteri, V. / Furihata, H. / Darren, D. / Ramachandran, S. / Rutter, Z.J. / Chakraborti, S. / Haubrich, K. / Pethe, J. / Gonzales, D. / Wijaya, A. / Rodriguez-Rios, M. / Lynch, D. / Farnaby, W. / Nakasone, M. / Zollman, D. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rqa.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rqa.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rqa_validation.pdf.gz | 728.1 KB | Display | wwPDB validaton report |
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Full document | 8rqa_full_validation.pdf.gz | 741.2 KB | Display | |
Data in XML | 8rqa_validation.xml.gz | 15 KB | Display | |
Data in CIF | 8rqa_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/8rqa ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rqa | HTTPS FTP |
-Related structure data
Related structure data | 8rq1C 8rq8C 8rq9C 8rqcC 9gaoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-LVY / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Tris pH 8, 20 % w/v PEG 4000, 1.2 % myo-inositol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 30, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6199 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.54 Å / Num. obs: 13030 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.046 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 1181 / CC1/2: 0.42 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.54 Å / SU ML: 0.4461 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.6099 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.54 Å
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Refine LS restraints |
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LS refinement shell |
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