+Open data
-Basic information
Entry | Database: PDB / ID: 7cyu | ||||||
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Title | Crystal structure of human BAF57 HMG domain | ||||||
Components | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 | ||||||
Keywords | DNA BINDING PROTEIN / Chromatin remodeling / SWI/SNF | ||||||
Function / homology | Function and homology information bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / N-acetyltransferase activity / SWI/SNF complex ...bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / N-acetyltransferase activity / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / 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 / positive regulation of myoblast differentiation / neurogenesis / nuclear receptor binding / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / transcription coactivator activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Heo, Y. / Yun, J.H. / Park, J.H. / Lee, W. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA. Authors: Heo, Y. / Park, J.H. / Kim, J. / Han, J. / Yun, J.H. / Lee, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cyu.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cyu.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 7cyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cyu ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cyu | HTTPS FTP |
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-Related structure data
Related structure data | 3tq6S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 8555.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1, BAF57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969G3 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.15 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.0M Ammonium sulfate, 0.1M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 3481 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 55.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.62 |
Reflection shell | Resolution: 2.55→2.59 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 312 / CC1/2: 0.844 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3tq6 Resolution: 2.55→35.79 Å / SU ML: 0.3541 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.7831 / Stereochemistry target values: 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: 58.54 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→35.79 Å
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Refine LS restraints |
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LS refinement shell |
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