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Yorodumi- PDB-4er5: Crystal structure of human DOT1L in complex with 2 molecules of E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4er5 | ||||||
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Title | Crystal structure of human DOT1L in complex with 2 molecules of EPZ004777 | ||||||
Components | Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase | ||||||
Keywords | Transferase/Transferase Inhibitor / histone / methyltransferase / epigenetics / Transferase-Transferase Inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization / DNA damage checkpoint signaling ...histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / gene expression / methylation / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / transcription coactivator activity / intracellular membrane-bounded organelle / DNA repair / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.57 Å | ||||||
Authors | Wernimont, A.K. / Tempel, W. / Yu, W. / Scopton, A. / Li, Y. / Nguyen, K.T. / Federation, A. / Marineau, J. / Qi, J. / Vedadi, M. ...Wernimont, A.K. / Tempel, W. / Yu, W. / Scopton, A. / Li, Y. / Nguyen, K.T. / Federation, A. / Marineau, J. / Qi, J. / Vedadi, M. / Bradner, J.E. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Brown, P.J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2012 Title: Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors. Authors: Yu, W. / Chory, E.J. / Wernimont, A.K. / Tempel, W. / Scopton, A. / Federation, A. / Marineau, J.J. / Qi, J. / Barsyte-Lovejoy, D. / Yi, J. / Marcellus, R. / Iacob, R.E. / Engen, J.R. / ...Authors: Yu, W. / Chory, E.J. / Wernimont, A.K. / Tempel, W. / Scopton, A. / Federation, A. / Marineau, J.J. / Qi, J. / Barsyte-Lovejoy, D. / Yi, J. / Marcellus, R. / Iacob, R.E. / Engen, J.R. / Griffin, C. / Aman, A. / Wienholds, E. / Li, F. / Pineda, J. / Estiu, G. / Shatseva, T. / Hajian, T. / Al-Awar, R. / Dick, J.E. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Bradner, J.E. / Schapira, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4er5.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4er5.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 4er5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/4er5 ftp://data.pdbj.org/pub/pdb/validation_reports/er/4er5 | HTTPS FTP |
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-Related structure data
Related structure data | 3uwpC 4eqzC 4er0C 4er3C 4er6C 4er7C C: citing same article (ref.) |
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Similar 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 MOLECULE IS UNKNOWN. |
-Components
#1: Protein | Mass: 47050.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DOT1L, KIAA1814, KMT4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 V2r Prare2 References: UniProt: Q8TEK3, histone-lysine N-methyltransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-UNX / #4: 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: 3.7 Å3/Da / Density % sol: 66.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 3.5 M NaFormate, 0.1 M NaAcet, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.57→49.243 Å / Num. all: 22277 / Num. obs: 22277 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Rsym value: 0.094 / Net I/σ(I): 21.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.57→49.24 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2102 / WRfactor Rwork: 0.1879 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8742 / SU B: 13.508 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2559 / SU Rfree: 0.2014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 98.73 Å2 / Biso mean: 52.7349 Å2 / Biso min: 27.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→49.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.57→2.637 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.6645 Å / Origin y: 57.9165 Å / Origin z: 2.9241 Å
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