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Yorodumi- PDB-6nm4: Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nm4 | ||||||
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Title | Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor | ||||||
Components | Histone-lysine N-methyltransferase PRDM9 | ||||||
Keywords | GENE REGULATION/INHIBITOR / PR SET domain / Lysine Methyltransferase / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / GENE REGULATION-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / 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 / methylation / regulation of gene expression / 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 / molecular replacement / Resolution: 2.58 Å | ||||||
Authors | Ivanochko, D. / Halabelian, L. / Fischer, C. / Sanders, J.M. / Kattar, S.D. / Brown, P.J. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Discovery of a chemical probe for PRDM9. Authors: Allali-Hassani, A. / Szewczyk, M.M. / Ivanochko, D. / Organ, S.L. / Bok, J. / Ho, J.S.Y. / Gay, F.P.H. / Li, F. / Blazer, L. / Eram, M.S. / Halabelian, L. / Dilworth, D. / Luciani, G.M. / ...Authors: Allali-Hassani, A. / Szewczyk, M.M. / Ivanochko, D. / Organ, S.L. / Bok, J. / Ho, J.S.Y. / Gay, F.P.H. / Li, F. / Blazer, L. / Eram, M.S. / Halabelian, L. / Dilworth, D. / Luciani, G.M. / Lima-Fernandes, E. / Wu, Q. / Loppnau, P. / Palmer, N. / Talib, S.Z.A. / Brown, P.J. / Schapira, M. / Kaldis, P. / O'Hagan, R.C. / Guccione, E. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Sanders, J.M. / Kattar, S.D. / Bennett, D.J. / Nicholson, B. / Vedadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nm4.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nm4.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/6nm4 ftp://data.pdbj.org/pub/pdb/validation_reports/nm/6nm4 | HTTPS FTP |
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-Related structure data
Related structure data | 4ijdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 196 - 377 / Label seq-ID: 2 - 183
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21802.352 Da / Num. of mol.: 2 / Fragment: PR-SET domain (UNP residues 195-385) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM9, PFM6 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NQV7, histone-lysine N-methyltransferase |
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-Non-polymers , 5 types, 32 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris, pH 6.0, 0.2 M ammonium acetate, 24.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018 | ||||||||||||||||||||||||
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.58→39.88 Å / Num. obs: 13290 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.051 / Rrim(I) all: 0.139 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4IJD Resolution: 2.58→39.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 29.499 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.759 / ESU R Free: 0.336 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.05 Å2 / Biso mean: 61.466 Å2 / Biso min: 30.37 Å2
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Refinement step | Cycle: final / Resolution: 2.58→39.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5587 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.58→2.647 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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