+Open data
-Basic information
Entry | Database: PDB / ID: 6s1r | ||||||||||||
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Title | Structure of fission yeast Mis16 bound to histone H4 | ||||||||||||
Components |
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Keywords | CELL CYCLE / centromere mitosis WD40 histone chaperone | ||||||||||||
Function / homology | Function and homology information PKMTs methylate histone lysines / HDMs demethylate histones / : / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HATs acetylate histones / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / CENP-A recruiting complex ...PKMTs methylate histone lysines / HDMs demethylate histones / : / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HATs acetylate histones / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / CENP-A recruiting complex / Neddylation / HDACs deacetylate histones / Estrogen-dependent gene expression / H3-H4 histone complex chaperone activity / RNA Polymerase I Promoter Escape / SUMOylation of chromatin organization proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Transcriptional regulation by small RNAs / Rpd3L complex / Rpd3L-Expanded complex / CENP-A containing chromatin assembly / NuRD complex / ESC/E(Z) complex / chromosome, centromeric region / nucleosome binding / kinetochore / nucleosome / nucleosome assembly / histone binding / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Lefevre, S. / Korntner-Vetter, M. / Singleton, M.R. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Life Sci Alliance / Year: 2019 Title: Subunit interactions and arrangements in the fission yeast Mis16-Mis18-Mis19 complex. Authors: Korntner-Vetter, M. / Lefevre, S. / Hu, X.W. / George, R. / Singleton, M.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s1r.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1r.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s1r_validation.pdf.gz | 442.5 KB | Display | wwPDB validaton report |
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Full document | 6s1r_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 6s1r_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6s1r_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1r ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1r | HTTPS FTP |
-Related structure data
Related structure data | 6s1lSC 6s29C 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: 48407.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: mis16, hat2, SPCC1672.10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O94244 |
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#2: Protein/peptide | Mass: 3476.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P09322 |
#3: 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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.05 M LiSO4, 0.8 M NaH2PO4, 1.2 M K2HPO4, 0.1 M CAPS pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.22 Å / Num. obs: 39885 / % possible obs: 96.58 % / Redundancy: 2 % / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 1.8→1.864 Å / Num. unique obs: 3857 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S1L Resolution: 1.8→46.22 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→46.22 Å
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Refine LS restraints |
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LS refinement shell |
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