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Yorodumi- PDB-5ei9: Human PRDM9 allele-A ZnF Domain with Associated Recombination Hot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ei9 | ||||||
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Title | Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence I | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Protein-DNA complex / recombination / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information recombination hotspot binding / positive regulation of reciprocal meiotic recombination / positive regulation of fertilization / male gamete generation / [histone H3]-lysine9 N-trimethyltransferase / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity ...recombination hotspot binding / positive regulation of reciprocal meiotic recombination / positive regulation of fertilization / male gamete generation / [histone H3]-lysine9 N-trimethyltransferase / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / female gamete generation / histone H3K36 trimethyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / histone H3K4 methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / PKMTs methylate histone lysines / Meiotic recombination / chromosome / regulation of gene expression / methylation / transcription cis-regulatory region binding / regulation of DNA-templated transcription / negative regulation of apoptotic process / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.921 Å | ||||||
Authors | Patel, A. / Horton, J.R. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: Genes Dev. / Year: 2016 Title: Structural basis for human PRDM9 action at recombination hot spots. Authors: Patel, A. / Horton, J.R. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ei9.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ei9.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ei9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ei9_validation.pdf.gz | 471.3 KB | Display | wwPDB validaton report |
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Full document | 5ei9_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | 5ei9_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5ei9_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/5ei9 ftp://data.pdbj.org/pub/pdb/validation_reports/ei/5ei9 | HTTPS FTP |
-Related structure data
-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: DNA chain | Mass: 6489.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: Protein | Mass: 16982.342 Da / Num. of mol.: 2 / Fragment: ZnF8-12 (UNP residues 717-858) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM9, PFM6 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon-plus RIL References: UniProt: Q9NQV7, histone-lysine N-methyltransferase #3: DNA chain | Mass: 6400.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-ZN / #5: 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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.058 M Bistris Propane, 0.042 M Citric acid, 25% PEG3350 PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jul 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→32.98 Å / Num. obs: 52634 / % possible obs: 99.9 % / Redundancy: 24.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.39 |
Reflection shell | Resolution: 1.92→2.02 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Zn SAD determined structure Resolution: 1.921→32.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.12 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.921→32.98 Å
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Refine LS restraints |
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LS refinement shell |
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