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Yorodumi- PDB-6bnb: Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bnb | ||||||||||||||||||
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Title | Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC | ||||||||||||||||||
Components |
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Keywords | LIGASE / PROTAC / degrader / E3 ligase / CRBN | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding ...negative regulation of monoatomic ion transmembrane transport / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / locomotory exploration behavior / cullin family protein binding / viral release from host cell / positive regulation of Wnt signaling pathway / ectopic germ cell programmed cell death / proteasomal protein catabolic process / negative regulation of protein-containing complex assembly / positive regulation of viral genome replication / positive regulation of gluconeogenesis / regulation of circadian rhythm / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / positive regulation of protein-containing complex assembly / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / rhythmic process / cellular response to UV / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / toxin activity / transmembrane transporter binding / damaged DNA binding / protein ubiquitination / DNA repair / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / apoptotic process / perinuclear region of cytoplasm / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.343 Å | ||||||||||||||||||
Authors | Nowak, R.P. / DeAngelo, S.L. / Buckley, D. / Ishoey, M. / He, Z. / Zhang, T. / Bradner, J.E. / Fischer, E.S. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Plasticity in binding confers selectivity in ligand-induced protein degradation. Authors: Nowak, R.P. / DeAngelo, S.L. / Buckley, D. / He, Z. / Donovan, K.A. / An, J. / Safaee, N. / Jedrychowski, M.P. / Ponthier, C.M. / Ishoey, M. / Zhang, T. / Mancias, J.D. / Gray, N.S. / ...Authors: Nowak, R.P. / DeAngelo, S.L. / Buckley, D. / He, Z. / Donovan, K.A. / An, J. / Safaee, N. / Jedrychowski, M.P. / Ponthier, C.M. / Ishoey, M. / Zhang, T. / Mancias, J.D. / Gray, N.S. / Bradner, J.E. / Fischer, E.S. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bnb.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bnb.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bnb_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 6bnb_full_validation.pdf.gz | 540 KB | Display | |
Data in XML | 6bnb_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 6bnb_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/6bnb ftp://data.pdbj.org/pub/pdb/validation_reports/bn/6bnb | HTTPS FTP |
-Related structure data
Related structure data | 6bn7C 6bn8C 6bn9C 6boyC 3mxfS 5fqdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 96425.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531 |
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#2: Protein | Mass: 53005.207 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SW2 |
#3: Protein | Mass: 15333.856 Da / Num. of mol.: 1 / Fragment: residues 42-168 / Mutation: T43M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 |
#4: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.24 Å3/Da / Density % sol: 80.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.34M NaH2PO4, 0.33M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97241 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97241 Å / Relative weight: 1 |
Reflection | Resolution: 6.34→156.68 Å / Num. obs: 8992 / % possible obs: 98.1 % / Redundancy: 25.4 % / CC1/2: 1 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.047 / Rrim(I) all: 0.172 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 6.34→7.08 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.952 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2370 / CC1/2: 0.627 / Rpim(I) all: 0.815 / Rrim(I) all: 3.063 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FQD chain A/B;3MXF chain A Resolution: 6.343→147.632 Å / SU ML: 0.94 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 46.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.343→147.632 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 6.343→6.57 Å
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