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Yorodumi- PDB-1nw3: Structure of the Catalytic domain of human DOT1L, a non-SET domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nw3 | ||||||
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Title | Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase | ||||||
Components | histone methyltransferase DOT1L | ||||||
Keywords | TRANSFERASE / hDot1 / histone lysine methyltransferase | ||||||
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 / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines ...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 / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / heterochromatin formation / gene expression / methylation / transcription coactivator activity / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / MAD / Resolution: 2.5 Å | ||||||
Authors | Min, J.R. / Feng, Q. / Li, Z.H. / Zhang, Y. / Xu, R.M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structure of the Catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase Authors: Min, J. / Feng, Q. / Li, Z. / Zhang, Y. / Xu, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nw3.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nw3.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nw3_validation.pdf.gz | 718.2 KB | Display | wwPDB validaton report |
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Full document | 1nw3_full_validation.pdf.gz | 722.2 KB | Display | |
Data in XML | 1nw3_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1nw3_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/1nw3 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/1nw3 | HTTPS FTP |
-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: 47506.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: dot1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8TEK3 | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | #4: Chemical | ChemComp-SAM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 71.82 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2002 / Details: Si monochromator | ||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 23805 / Num. obs: 22926 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 18.3 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 23800 / Num. measured all: 175389 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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