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Yorodumi- PDB-4c1q: Crystal structure of the PRDM9 SET domain in complex with H3K4me2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1q | ||||||
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Title | Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy. | ||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / HISTONE METHYLTRANSFERASE / SET DOMAIN H3K4ME3 | ||||||
Function / homology | Function and homology information : / : / : / : / : / : / recombination hotspot binding / : / : / : ...: / : / : / : / : / : / recombination hotspot binding / : / : / : / Generic Transcription Pathway / : / : / positive regulation of reciprocal meiotic recombination / : / : / positive regulation of fertilization / [histone H3]-lysine9 N-trimethyltransferase / male gamete generation / meiotic gene conversion / [histone H4]-N-methyl-L-lysine20 N-methyltransferase / positive regulation of meiosis I / [histone H4]-lysine20 N-methyltransferase / [histone H3]-lysine36 N-trimethyltransferase / female gamete generation / [histone H3]-lysine4 N-trimethyltransferase / PKMTs methylate histone lysines / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone methyltransferase activity / telomere organization / Chromatin modifying enzymes / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Transferases; Transferring one-carbon groups; Methyltransferases / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Factors involved in megakaryocyte development and platelet production / nucleosome assembly / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of gene expression / HATs acetylate histones / gene expression / spermatogenesis / Oxidative Stress Induced Senescence / sequence-specific DNA binding / Estrogen-dependent gene expression / transcription cis-regulatory region binding / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Mathioudakis, N. / Cusack, S. / Kadlec, J. | ||||||
Citation | Journal: Cell Rep. / Year: 2013 Title: Molecular Basis for the Regulation of the H3K4 Methyltransferase Activity of Prdm9. Authors: Wu, H. / Mathioudakis, N. / Diagouraga, B. / Dong, A. / Dombrovski, L. / Baudat, F. / Cusack, S. / De Massy, B. / Kadlec, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c1q.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1q.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4c1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1q ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1q | HTTPS FTP |
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-Related structure data
Related structure data | 3rayS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (0.998392, 0.034147, -0.045252), Vector: |
-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 19899.029 Da / Num. of mol.: 2 / Fragment: SET DOMAIN, RESIDUES 198-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: Q96EQ9, histone-lysine N-methyltransferase #2: Protein/peptide | | Mass: 1253.474 Da / Num. of mol.: 1 / Fragment: N-TERMINUS, RESIDUES 2-11 / Source method: obtained synthetically / Details: DOUBLE METHYLATION ON LYSINE 4 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431 |
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-Non-polymers , 4 types, 65 molecules
#3: Chemical | ChemComp-SAH / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion / pH: 5.5 Details: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5 AND 25% W/V PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.939 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 21499 / % possible obs: 99.5 % / Observed criterion σ(I): 2.3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RAY Resolution: 2.3→49.54 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.231 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.54 Å
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Refine LS restraints |
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