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Yorodumi- PDB-4m6b: Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m6b | ||||||
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Title | Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer | ||||||
Components |
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Keywords | Structural Protein/Hydrolase / Chromatin remodeler / Histone binding / Structural Protein-Hydrolase complex | ||||||
Function / homology | Function and homology information Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / Swr1 complex / replication fork protection complex / recombinational repair / postreplication repair / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / helicase activity / euchromatin ...Condensation of Prophase Chromosomes / nuclear-transcribed mRNA catabolic process, non-stop decay / Swr1 complex / replication fork protection complex / recombinational repair / postreplication repair / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / helicase activity / euchromatin / chromatin DNA binding / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / DNA helicase / molecular adaptor activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / chromatin / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Hong, J.J. / Feng, H.Q. / Wang, F. / Ranjan, A. / Chen, J.H. / Jiang, J.S. / Girlando, R. / Xiao, T.S. / Wu, C. / Bai, Y.W. | ||||||
Citation | Journal: Mol.Cell / Year: 2014 Title: The Catalytic Subunit of the SWR1 Remodeler Is a Histone Chaperone for the H2A.Z-H2B Dimer. Authors: Hong, J. / Feng, H. / Wang, F. / Ranjan, A. / Chen, J. / Jiang, J. / Ghirlando, R. / Xiao, T.S. / Wu, C. / Bai, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m6b.cif.gz | 94.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m6b.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/4m6b ftp://data.pdbj.org/pub/pdb/validation_reports/m6/4m6b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21205.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C, HTZ1, H2AZ, HTA3, YOL012C, O2345 Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus(DE3)-RIPL / References: UniProt: P02293, UniProt: Q12692 #2: Protein | Mass: 5970.131 Da / Num. of mol.: 2 / Fragment: Swr1-Z domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SWR1, YDR334W, D9651.6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codonplus(DE3)-RIPL / References: UniProt: Q05471, DNA helicase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% (w/v) PEG 2000 MME, 100 mM HEPES, pH 7.5, 50 mM Calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 274 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 45391 / Num. obs: 43986 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 75.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å
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