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Yorodumi- PDB-6haz: Crystal structure of the bromodomain of human SMARCA2 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6haz | ||||||
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Title | Crystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand | ||||||
Components | Probable global transcription activator SNF2L2 | ||||||
Keywords | GENE REGULATION / bromodomain | ||||||
Function / homology | Function and homology information bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex ...bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / intermediate filament cytoskeleton / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / spermatid development / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / helicase activity / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of cell growth / RMTs methylate histone arginines / nervous system development / histone binding / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Bader, G. / Steurer, S. / Weiss-Puxbaum, A. / Zoephel, A. / Roy, M. / Ciulli, A. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / ...Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / Galant, M. / Sharps, B. / Rumpel, K. / Traxler, E. / Gerstberger, T. / Schnitzer, R. / Petermann, O. / Greb, P. / Weinstabl, H. / Bader, G. / Zoephel, A. / Weiss-Puxbaum, A. / Ehrenhofer-Wolfer, K. / Wohrle, S. / Boehmelt, G. / Rinnenthal, J. / Arnhof, H. / Wiechens, N. / Wu, M.Y. / Owen-Hughes, T. / Ettmayer, P. / Pearson, M. / McConnell, D.B. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6haz.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6haz.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 6haz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6haz ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6haz | HTTPS FTP |
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-Related structure data
Related structure data | 6haxC 6hayC 6hr2C 4qy4S 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: 14380.542 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | #4: 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: 2.81 Å3/Da / Density % sol: 56.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 25% (w/v) PEG 6000, 0.1 M HEPES, pH 6.1, 0.01M zinc chloride, 0.01 M cobalt (III) hexamine chloride, 8% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99993 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→42.549 Å / Num. obs: 66651 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.31→1.476 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2249 / CC1/2: 0.6 / Rpim(I) all: 0.497 / Rrim(I) all: 1.177 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QY4 Resolution: 1.31→26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.065 / Details: Hydrogens included in refinement.
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Displacement parameters | Biso max: 145.92 Å2 / Biso mean: 27.14 Å2 / Biso min: 8.55 Å2
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Refine analyze | Luzzati coordinate error obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.31→1.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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