+Open data
-Basic information
Entry | Database: PDB / ID: 2j8a | ||||||
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Title | X-ray structure of the N-terminus RRM domain of Set1 | ||||||
Components | HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFICHistone methyltransferase | ||||||
Keywords | TRANSFERASE / HISTONE METHYLTRANSFERASE / RRM FOLD / TELOMERE / NUCLEAR PROTEIN / METHYLTRANSFERASE / CHROMOSOMAL PROTEIN | ||||||
Function / homology | Function and homology information : / positive regulation of synaptonemal complex assembly / : / : / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / : / meiotic DNA double-strand break formation / ascospore formation ...: / positive regulation of synaptonemal complex assembly / : / : / regulation of meiotic DNA double-strand break formation / Formation of WDR5-containing histone-modifying complexes / : / : / meiotic DNA double-strand break formation / ascospore formation / sterol homeostasis / [histone H3]-lysine4 N-trimethyltransferase / regulation of chromatin organization / synaptonemal complex assembly / histone H3K4 trimethyltransferase activity / protein methylation / rDNA heterochromatin formation / protein-lysine N-methyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / telomere maintenance / chromosome, telomeric region / negative regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å | ||||||
Authors | Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. ...Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V. | ||||||
Citation | Journal: To be Published Title: X-Ray Structure of the N-Terminus Rrm Domain of Set1 Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / ...Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V. #1: Journal: J.Mol.Biol. / Year: 2006 Title: Structural Characterization of Set1 RNA Recognition Motifs and Their Role in Histone H3 Lysine 4 Methylation. Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / ...Authors: Tresaugues, L. / Dehe, P.M. / Guerois, R. / Rodriguez-Gil, A. / Varlet, I. / Salah, P. / Pamblanco, M. / Luciano, P. / Quevillon-Cheruel, S. / Sollier, J. / Leulliot, N. / Couprie, J. / Tordera, V. / Zinn-Justin, S. / Chavez, S. / Van Tilbeurgh, H. / Geli, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j8a.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j8a.ent.gz | 25.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j8a ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j8a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15568.778 Da / Num. of mol.: 1 / Fragment: N-TERMINUS RRM DOMAIN, RESIDUES 247-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S228C / Plasmid: PET-9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GOLD References: UniProt: P38827, histone-lysine N-methyltransferase |
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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: 5.67 Å3/Da / Density % sol: 75.2 % |
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Crystal grow | pH: 4.6 Details: 2.15M AMMONIUM SULFATE,50MM NACITRATE PH4.6,4% POLYPROPYLENE-GLYCOL 400,3% GLYCEROL, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.5 Å / Num. obs: 7192 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.877 / SU B: 12.12 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 302-306 AND 367-CTERMINUS ARE DISORDERED
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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: 67.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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