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- PDB-3uvd: Crystal Structure of the bromodomain of human Transcription activ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uvd | ||||||
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Title | Crystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in complex with N-Methyl-2-pyrrolidone | ||||||
![]() | Transcription activator BRG1 | ||||||
![]() | TRANSCRIPTION / 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 | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / 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 | ![]() | 66.6 KB | Display | ![]() |
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PDB format | ![]() | 48.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.4 KB | Display | ![]() |
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Full document | ![]() | 445 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbC ![]() 2oo1SC ![]() 2ossSC ![]() 2ouoSC ![]() 2rfjC ![]() 3d7cSC ![]() 3daiSC ![]() 3dwySC ![]() 3gg3SC ![]() 3hmeC ![]() 3hmfC ![]() 3hmhC ![]() 3i3jC ![]() 3iu5C ![]() 3iu6C ![]() 3lxjC ![]() 3mb3C ![]() 3mb4C ![]() 3mqmC ![]() 3nxbC ![]() 3p1cC ![]() 3p1dC ![]() 3q2eC ![]() 3rcwC ![]() 3tlpC ![]() 3uv2C ![]() 3uv4C ![]() 3uv5C ![]() 3uvwC ![]() 3uvxC ![]() 3uvyC ![]() 3uw9C ![]() 2grcS ![]() 3g0jS ![]() 3g0lS C: citing same article ( 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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Unit cell |
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Details | monomer |
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Components
#1: Protein | Mass: 14559.822 Da / Num. of mol.: 1 / Fragment: unp residues 1448-1569 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 |
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#2: Chemical | ChemComp-MB3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 28% MMW PEG smear 0.1M Tris.HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.52 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.5 % / Av σ(I) over netI: 4.2 / Number: 36801 / Rsym value: 0.067 / D res high: 1.85 Å / D res low: 29.89 Å / Num. obs: 10488 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.85→29.89 Å / Num. all: 10488 / Num. obs: 10488 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 52.46 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3 Resolution: 1.85→29.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2907 / WRfactor Rwork: 0.2228 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7914 / SU B: 8.559 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1611 / SU Rfree: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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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 max: 152.18 Å2 / Biso mean: 46.1641 Å2 / Biso min: 18.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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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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