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- PDB-5dkd: Crystal structure of the bromodomain of human BRG1 (SMARCA4) in c... -
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Basic information
Entry | Database: PDB / ID: 5dkd | ||||||
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Title | Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe | ||||||
![]() | Transcription activator BRG1 | ||||||
![]() | HYDROLASE / SWI-SNF complex / chromatin remodeling / Brg associated factors (BAF) / transcription | ||||||
Function / homology | ![]() positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition ...positive regulation of glucose mediated signaling pathway / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome disassembly / 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 / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / 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 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 / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / positive regulation of DNA-binding transcription factor activity / nuclear matrix / positive regulation of miRNA transcription / transcription corepressor activity / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. ...Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S. | ||||||
![]() | ![]() Title: Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / ...Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uvdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1457 - 1566 / Label seq-ID: 9 - 118
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Components
#1: Protein | Mass: 14230.447 Da / Num. of mol.: 2 / Fragment: UNP residues 1418-1536 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.78 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k) PH range: 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9207 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.78 Å / Num. obs: 21859 / % possible obs: 96.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.054 / Net I/av σ(I): 9.8 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.3 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3UVD Resolution: 2→29.78 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.829 / SU B: 9.907 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refinement step | Cycle: 1 / Resolution: 2→29.78 Å
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Refine LS restraints |
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