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Yorodumi- PDB-5ii2: Crystal Structure of the fifth bromodomain of human polybromo (PB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ii2 | ||||||
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Title | Crystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one | ||||||
Components | Protein polybromo-1 | ||||||
Keywords | TRANSCRIPTION / bromodomain / complex / small molecule / structural genomics consortium / SGC | ||||||
Function / homology | Function and homology information regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Filippakopoulos, P. / Picaud, S. / Felletar, I. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis. Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / ...Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / Savitsky, P. / Bagratuni, T. / Kastritis, E. / Terpos, E. / Filippakopoulos, P. / Muller, S. / Skaltsounis, A.L. / Downs, J.A. / Knapp, S. / Mikros, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ii2.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ii2.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ii2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ii2_validation.pdf.gz | 932.3 KB | Display | wwPDB validaton report |
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Full document | 5ii2_full_validation.pdf.gz | 932.5 KB | Display | |
Data in XML | 5ii2_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5ii2_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5ii2 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5ii2 | HTTPS FTP |
-Related structure data
Related structure data | 5hrvC 5hrwC 5hrxC 5ii1C 5iidC 2grcS 2ossS 2ouoS 3d7cS 3daiS 3dwyS 3hmhS 3mb4S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14648.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q86U86 #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.20M K3(cit) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→24.186 Å / Num. obs: 20237 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/av σ(I): 3.929 / Net I/σ(I): 9.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY Resolution: 2.1→24.186 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.205 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.162 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.33 Å2 / Biso mean: 28.073 Å2 / Biso min: 14.17 Å2
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Refinement step | Cycle: final / Resolution: 2.1→24.186 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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