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Yorodumi- PDB-2kkf: Solution structure of MLL CXXC domain in complex with palindromic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kkf | ||||||
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Title | Solution structure of MLL CXXC domain in complex with palindromic CPG DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / CXXC DOMAIN / MLL / CPG DNA / CHROMOSOMAL REARRANGEMENT / DNA-BINDING / METAL-BINDING / NUCLEUS / ZINC-FINGER / DNA BINDING PROTEIN-DNA COMPLEX / Alternative splicing / Apoptosis / Bromodomain / Chromatin regulator / Isopeptide bond / Methyltransferase / Phosphoprotein / Polymorphism / Proto-oncogene / S-adenosyl-L-methionine / Transcription / Transcription regulation / Transferase / Ubl conjugation / Zinc | ||||||
Function / homology | Function and homology information protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / exploration behavior / definitive hemopoiesis / histone H3K4 methyltransferase activity ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / exploration behavior / definitive hemopoiesis / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / embryonic hemopoiesis / anterior/posterior pattern specification / histone methyltransferase complex / : / Formation of WDR5-containing histone-modifying complexes / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / epigenetic regulation of gene expression / spleen development / transcription initiation-coupled chromatin remodeling / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / visual learning / circadian regulation of gene expression / protein modification process / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Transcriptional regulation of granulopoiesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / fibroblast proliferation / protein-containing complex assembly / apoptotic process / chromatin binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, DISTANCE GEOMETRY | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Cierpicki, T. / Riesbeck, J.E. / Grembecka, J.E. / Lukasik, S.M. / Popovic, R. / Omonkowska, M. / Shultis, D.S. / Zeleznik-Le, N.J. / Bushweller, J.H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structure of the MLL CXXC domain-DNA complex and its functional role in MLL-AF9 leukemia. Authors: Cierpicki, T. / Risner, L.E. / Grembecka, J. / Lukasik, S.M. / Popovic, R. / Omonkowska, M. / Shultis, D.D. / Zeleznik-Le, N.J. / Bushweller, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kkf.cif.gz | 348.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kkf.ent.gz | 297 KB | Display | PDB format |
PDBx/mmJSON format | 2kkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/2kkf ftp://data.pdbj.org/pub/pdb/validation_reports/kk/2kkf | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 6677.991 Da / Num. of mol.: 1 / Fragment: CXXC DOMAIN: UNP RESIDUES 1147-1203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, TRX1 / Plasmid: pGEX4-T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q03164, histone-lysine N-methyltransferase | ||
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#2: DNA chain | Mass: 3664.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Palindromic DNA #3: Chemical | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 25 / pH: 7.0 / Pressure: Ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, DISTANCE GEOMETRY / Software ordinal: 1 Details: HIGH TEMP ANNEALING WITHOUT RRDCS, LOW TEMP ANNEALING WITH RDCS | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |