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Yorodumi- PDB-6j2p: Crystal structure of Saccharomyces cerevisiae Spp1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j2p | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 | ||||||
Components |
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Keywords | PROTEIN BINDING / Histone modification recognition | ||||||
Function / homology | Function and homology information regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Set1C/COMPASS complex / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / subtelomeric heterochromatin formation ...regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Set1C/COMPASS complex / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / subtelomeric heterochromatin formation / rRNA transcription / CENP-A containing nucleosome / methylated histone binding / structural constituent of chromatin / nucleosome / chromatin organization / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å | ||||||
Authors | He, C. / Li, F. | ||||||
Citation | Journal: Biochem.J. / Year: 2019 Title: Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1. Authors: He, C. / Liu, N. / Xie, D. / Liu, Y. / Xiao, Y. / Li, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j2p.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j2p.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/6j2p ftp://data.pdbj.org/pub/pdb/validation_reports/j2/6j2p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 14246.196 Da / Num. of mol.: 4 / Fragment: UNP residues 1-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: SPP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03012 #2: Protein/peptide | Mass: 818.961 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P61830 #3: Chemical | ChemComp-ZN / |
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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: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→69.915 Å / Num. all: 14530 / Num. obs: 14530 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 69.48 Å2 / Rpim(I) all: 0.056 / Rrim(I) all: 0.132 / Rsym value: 0.119 / Net I/av σ(I): 5.4 / Net I/σ(I): 8.8 / Num. measured all: 77725 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.85→42.279 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.8 / Stereochemistry target values: ML
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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 max: 169.47 Å2 / Biso mean: 78.3615 Å2 / Biso min: 31.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→42.279 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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