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Yorodumi- PDB-6zs2: Crystal Structure of the bromodomain of human transcription activ... -
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-Basic information
Entry | Database: PDB / ID: 6zs2 | ||||||
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Title | Crystal Structure of the bromodomain of human transcription activator BRG1 (SMARCA4) in complex with 2-(6-amino-5-(piperazin-1-yl)pyridazin-3-yl)phenol | ||||||
Components | Transcription activator BRG1 | ||||||
Keywords | GENE REGULATION / BROMODOMAIN / ATP-DEPENDENT HELICASE SMARCA4 / BRG1-ASSOCIATED FACTOR 190A / BAF190A / MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR / PROTEIN BRG-1 / PROTEIN BRAHMA HOMOLOG 1 / SNF2-BETA / SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY A MEMBER 4 / STRUCTURAL GENOMICS CONSORTIUM / SGC / TRANSCRIPTION | ||||||
Function / homology | Function and homology information positive regulation of glucose mediated signaling pathway / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development ...positive regulation of glucose mediated signaling pathway / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of nucleotide-excision repair / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / positive regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription coregulator binding / helicase activity / positive regulation of cell differentiation / positive regulation of DNA-binding transcription factor activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / negative regulation of cell growth / fibrillar center / kinetochore / RMTs methylate histone arginines / positive regulation of miRNA transcription / nuclear matrix / transcription corepressor activity / positive regulation of cold-induced thermogenesis / p53 binding / nervous system development / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / nucleolus / 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 / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Preuss, F. / Joerger, A.C. / Kraemer, A. / Wanior, M. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis. Authors: Wanior, M. / Preuss, F. / Ni, X. / Kramer, A. / Mathea, S. / Gobel, T. / Heidenreich, D. / Simonyi, S. / Kahnt, A.S. / Joerger, A.C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zs2.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zs2.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zs2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zs2_validation.pdf.gz | 963.5 KB | Display | wwPDB validaton report |
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Full document | 6zs2_full_validation.pdf.gz | 963.5 KB | Display | |
Data in XML | 6zs2_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6zs2_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zs2 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zs2 | HTTPS FTP |
-Related structure data
Related structure data | 6zn6C 6znvC 6zs3C 6zs4C 5dkdS 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: 14230.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli) References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystallization buffer: 20% medium-molecular-weight PEG smear, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91842 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91842 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→47.3 Å / Num. obs: 35278 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.1272343356 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.57→1.6 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 1915 / CC1/2: 0.973 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DKD Resolution: 1.57→34.2487331998 Å / SU ML: 0.14241308346 / Cross valid method: FREE R-VALUE / σ(F): 1.36039202951 / Phase error: 23.1847411695 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.3242338323 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→34.2487331998 Å
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Refine LS restraints |
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LS refinement shell |
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