+Open data
-Basic information
Entry | Database: PDB / ID: 3s8s | ||||||
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Title | Crystal structure of the RRM domain of human SETD1A | ||||||
Components | Histone-lysine N-methyltransferase SETD1A | ||||||
Keywords | TRANSCRIPTION / chromatin modification / transcription regulation / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / regulation of hematopoietic stem cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / brain development ...regulation of chromatin organization / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / Set1C/COMPASS complex / histone H3K4 methyltransferase activity / regulation of hematopoietic stem cell differentiation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / brain development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / beta-catenin binding / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear speck / DNA damage response / chromatin / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Chao, X. / Tempel, W. / Bian, C. / Cerovina, T. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of the RRM domain of human SETD1A Authors: Chao, X. / Tempel, W. / Bian, C. / Cerovina, T. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s8s.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s8s.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8s ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
-Components
#1: Protein | Mass: 12486.447 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD1A, KIAA0339, KMT2F, SET1, SET1A / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O15047 | ||
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#2: Chemical | ChemComp-UNX / #3: 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: 1.61 Å3/Da / Density % sol: 23.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 1.5 M ammonium sulfate, 0.1 M bistris propane, pH 7.0, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97941 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97941 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→31.29 Å / Num. obs: 19651 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.625 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.39 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: composite of pdb entries 3LPY and 2J8A Resolution: 1.3→31.29 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.95 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs BUCCANEER and COOT were also used during refinement. The MOLPROBITY server was used for model geometry validation. Significant ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs BUCCANEER and COOT were also used during refinement. The MOLPROBITY server was used for model geometry validation. Significant difference density remains for the current model around the side chain of residue His-166.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→31.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.33 Å / Total num. of bins used: 20
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