+Open data
-Basic information
Entry | Database: PDB / ID: 6eg3 | ||||||
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Title | Crystal structure of human BRM in complex with compound 15 | ||||||
Components | Maltose/maltodextrin-binding periplasmic protein,Probable global transcription activator SNF2L2 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Helicase / ATPase / Chromatin remodeling / inhibitor / MBP fusion / Hydrolase-Hydrolase Inhibitor complex | ||||||
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 / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition ...bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / 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 / spermatid development / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / 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 / outer membrane-bounded periplasmic space / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / 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 | Escherichia coli O157:H7 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Zhu, X. / Kulathila, R. / Hu, T. / Xie, X. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers. Authors: Papillon, J.P.N. / Nakajima, K. / Adair, C.D. / Hempel, J. / Jouk, A.O. / Karki, R.G. / Mathieu, S. / Mobitz, H. / Ntaganda, R. / Smith, T. / Visser, M. / Hill, S.E. / Hurtado, F.K. / ...Authors: Papillon, J.P.N. / Nakajima, K. / Adair, C.D. / Hempel, J. / Jouk, A.O. / Karki, R.G. / Mathieu, S. / Mobitz, H. / Ntaganda, R. / Smith, T. / Visser, M. / Hill, S.E. / Hurtado, F.K. / Chenail, G. / Bhang, H.C. / Bric, A. / Xiang, K. / Bushold, G. / Gilbert, T. / Vattay, A. / Dooley, J. / Costa, E.A. / Park, I. / Li, A. / Farley, D. / Lounkine, E. / Yue, Q.K. / Xie, X. / Zhu, X. / Kulathila, R. / King, D. / Hu, T. / Vulic, K. / Cantwell, J. / Luu, C. / Jagani, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eg3.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eg3.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 6eg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/6eg3 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/6eg3 | HTTPS FTP |
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-Related structure data
Related structure data | 6eg2C 1fqaS 5hzrS 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: 69653.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, Z5632, ECs5017, SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 Production host: Escherichia coli (E. coli) References: UniProt: P0AEY0, UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||
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#2: Chemical | ChemComp-J7G / | ||
#3: Chemical | ChemComp-EOH / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM Tris pH7, 14% Ethanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→136.47 Å / Num. obs: 27552 / % possible obs: 100 % / Redundancy: 13.1 % / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.84→2.85 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FQA, 5HZR Resolution: 2.84→96.5 Å / Cor.coef. Fo:Fc: 0.8925 / Cor.coef. Fo:Fc free: 0.8739 / SU R Cruickshank DPI: 0.515 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.505 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.32
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Displacement parameters | Biso max: 153.59 Å2 / Biso mean: 78.03 Å2 / Biso min: 17.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.453 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.84→96.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.84→2.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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