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Yorodumi- PDB-6bgg: Solution NMR structures of the BRD3 ET domain in complex with a C... -
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-Basic information
Entry | Database: PDB / ID: 6bgg | ||||||
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Title | Solution NMR structures of the BRD3 ET domain in complex with a CHD4 peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / transcription regulation / epigenetics | ||||||
Function / homology | Function and homology information cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / lncRNA binding / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / endodermal cell differentiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / regulation of stem cell differentiation / NuRD complex / NGF-stimulated transcription / lncRNA binding / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / endodermal cell differentiation / site of DNA damage / RNA Polymerase I Transcription Initiation / protein localization to chromatin / Regulation of TP53 Activity through Acetylation / helicase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / molecular condensate scaffold activity / Regulation of PTEN gene transcription / transcription coregulator binding / HDACs deacetylate histones / double-strand break repair via homologous recombination / lysine-acetylated histone binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Lu, B. ...Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Lu, B. / Vakoc, C.R. / Blobel, G.A. / Mackay, J.P. | ||||||
Funding support | Australia, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. Authors: Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L.E. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Chalmers, J.D. / Patrick, W.M. / Lu, B. / ...Authors: Wai, D.C.C. / Szyszka, T.N. / Campbell, A.E. / Kwong, C. / Wilkinson-White, L.E. / Silva, A.P.G. / Low, J.K.K. / Kwan, A.H. / Gamsjaeger, R. / Chalmers, J.D. / Patrick, W.M. / Lu, B. / Vakoc, C.R. / Blobel, G.A. / Mackay, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bgg.cif.gz | 634.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bgg.ent.gz | 533.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bgg_validation.pdf.gz | 475.9 KB | Display | wwPDB validaton report |
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Full document | 6bgg_full_validation.pdf.gz | 699 KB | Display | |
Data in XML | 6bgg_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 6bgg_validation.cif.gz | 60.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/6bgg ftp://data.pdbj.org/pub/pdb/validation_reports/bg/6bgg | HTTPS FTP |
-Related structure data
Related structure data | 6bghC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1273.629 Da / Num. of mol.: 1 / Fragment: unp residues 290-301 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14839*PLUS |
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#2: Protein | Mass: 10687.956 Da / Num. of mol.: 1 / Fragment: unp residues 557-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q15059 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: .2 M / Label: 298 K pH 6.5 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Water refinement using RECOORD protocol (Nederveen 2015) | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |