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Yorodumi- PDB-2odd: Solution structure of the MYND domain from AML1-ETO complexed wit... -
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-Basic information
Entry | Database: PDB / ID: 2odd | ||||||
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Title | Solution structure of the MYND domain from AML1-ETO complexed with SMRT, a corepressor | ||||||
Components |
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Keywords | METAL BINDING PROTEIN / MYND zinc finger / cross-braced topology / poly-proline / proline-tryptophan interaction | ||||||
Function / homology | Function and homology information Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fat cell differentiation / Notch-HLH transcription pathway / nuclear retinoid X receptor binding / Regulation of MECP2 expression and activity ...Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fat cell differentiation / Notch-HLH transcription pathway / nuclear retinoid X receptor binding / Regulation of MECP2 expression and activity / estrous cycle / negative regulation of miRNA transcription / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / : / transcription repressor complex / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / SUMOylation of transcription cofactors / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / HCMV Early Events / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / transcription corepressor activity / response to estradiol / DNA-binding transcription factor binding / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Liu, Y.Z. / Chen, W. / Gaudet, J. / Cheney, M.D. / Roudaia, L. / Cierpicki, T. / Klet, R.C. / Hartman, K. / Laue, T.M. / Speck, N.A. / Bushweller, J.H. | ||||||
Citation | Journal: Cancer Cell / Year: 2007 Title: Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity. Authors: Liu, Y. / Chen, W. / Gaudet, J. / Cheney, M.D. / Roudaia, L. / Cierpicki, T. / Klet, R.C. / Hartman, K. / Laue, T.M. / Speck, N.A. / 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 | 2odd.cif.gz | 457.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2odd.ent.gz | 378.9 KB | Display | PDB format |
PDBx/mmJSON format | 2odd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2odd_validation.pdf.gz | 354.5 KB | Display | wwPDB validaton report |
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Full document | 2odd_full_validation.pdf.gz | 654.6 KB | Display | |
Data in XML | 2odd_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 2odd_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2odd ftp://data.pdbj.org/pub/pdb/validation_reports/od/2odd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1613.790 Da / Num. of mol.: 1 / Fragment: SMRT (residues 1101-1113) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMRT / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q9Y618*PLUS |
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#2: Protein | Mass: 7361.001 Da / Num. of mol.: 1 / Fragment: MYND domain (AML1-ETO, residues 658-707) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AML1-ETO / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q06455 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Details | Contents: 2mM SMRT-MYND, 25mM Bis-Tris, pH 6.8, 50uM ZnCl2, 1mM DTT, 95%H2O, 5% D2O Solvent system: 95% H2O/5% D2O |
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Sample conditions | pH: 6.8 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 25 |