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- PDB-5egb: Human PRDM9 allele-A ZnF Domain with Associated Recombination Hot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5egb | ||||||
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Title | Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II | ||||||
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![]() | TRANSCRIPTION/DNA / protein-DNA complex / zinc finger protein / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() recombination hotspot binding / positive regulation of reciprocal meiotic recombination / positive regulation of fertilization / [histone H3]-lysine9 N-trimethyltransferase / male gamete generation / histone H4K20me methyltransferase activity / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity ...recombination hotspot binding / positive regulation of reciprocal meiotic recombination / positive regulation of fertilization / [histone H3]-lysine9 N-trimethyltransferase / male gamete generation / histone H4K20me methyltransferase activity / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H3K9 trimethyltransferase activity / [histone H4]-lysine20 N-methyltransferase / [histone H3]-lysine36 N-trimethyltransferase / female gamete generation / histone H3K36 trimethyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / histone H3K4 trimethyltransferase activity / histone H3K36 methyltransferase 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of apoptotic process / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Patel, A. / Horton, J.R. / Wilson, G.G. / Zhang, X. / Cheng, X. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.6 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.6 KB | Display | ![]() |
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Full document | ![]() | 445.1 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6489.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
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#2: DNA chain | Mass: 6400.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||
#3: Protein | Mass: 16982.342 Da / Num. of mol.: 1 / Fragment: ZnF8-12 (UNP residues 717-858) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NQV7, histone-lysine N-methyltransferase | ||
#4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.055M Bis-Tris propane, 0.045M Citric Acid, 30% PEG3350 PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→29.64 Å / Num. obs: 22386 / % possible obs: 86.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 1.9 / % possible all: 37.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Zn SAD determined structure Resolution: 1.977→29.639 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.02 / 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: 1.977→29.639 Å
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Refine LS restraints |
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LS refinement shell |
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