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Yorodumi- PDB-2agh: Structural basis for cooperative transcription factor binding to ... -
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-Basic information
Entry | Database: PDB / ID: 2agh | ||||||
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Title | Structural basis for cooperative transcription factor binding to the CBP coactivator | ||||||
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Keywords | TRANSCRIPTION | ||||||
Function / homology | Function and homology information positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / myeloid cell development / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / myeloid cell development / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of hepatic stellate cell activation / protein-cysteine methyltransferase activity / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / positive regulation of transforming growth factor beta production / response to potassium ion / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / Cytoprotection by HMOX1 / embryonic digestive tract development / unmethylated CpG binding / stem cell division / CD209 (DC-SIGN) signaling / histone H3K4 trimethyltransferase activity / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / negative regulation of DNA methylation-dependent heterochromatin formation / myeloid cell differentiation / negative regulation of interferon-beta production / regulation of short-term neuronal synaptic plasticity / histone H3K18 acetyltransferase activity / cellular response to interleukin-6 / N-terminal peptidyl-lysine acetylation / T-helper 2 cell differentiation / histone H3K27 acetyltransferase activity / definitive hemopoiesis / MRF binding / histone H3K4 methyltransferase activity / peroxisome proliferator activated receptor binding / face morphogenesis / embryonic hemopoiesis / negative regulation of transcription by RNA polymerase I / exploration behavior / WD40-repeat domain binding / anterior/posterior pattern specification / histone methyltransferase complex / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of dendritic spine development / Formation of WDR5-containing histone-modifying complexes / SMAD binding / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / behavioral response to cocaine / acetyltransferase activity / MLL1 complex / TFIIB-class transcription factor binding / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / histone acetyltransferase complex / positive regulation of collagen biosynthetic process / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / negative regulation of fibroblast proliferation / histone acetyltransferase activity / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / histone acetyltransferase / spleen development / transcription initiation-coupled chromatin remodeling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cellular response to transforming growth factor beta stimulus / Transferases; Transferring one-carbon groups; Methyltransferases / B cell differentiation / post-embryonic development / thymus development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / circadian regulation of gene expression / protein destabilization / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / visual learning / protein modification process / chromatin DNA binding / PKMTs methylate histone lysines / cellular response to virus / PML body / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | De Guzman, R.N. / Goto, N.K. / Dyson, H.J. / Wright, P.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis for Cooperative Transcription Factor Binding to the CBP Coactivator Authors: De Guzman, R.N. / Goto, N.K. / Dyson, H.J. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2agh.cif.gz | 905.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2agh.ent.gz | 763.4 KB | Display | PDB format |
PDBx/mmJSON format | 2agh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2agh_validation.pdf.gz | 375.4 KB | Display | wwPDB validaton report |
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Full document | 2agh_full_validation.pdf.gz | 622.7 KB | Display | |
Data in XML | 2agh_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 2agh_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2agh ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2agh | 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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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2947.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myb / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06876 |
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#2: Protein | Mass: 10353.856 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: CBP, CREBBP / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45481 |
#3: Protein/peptide | Mass: 3309.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLL, ALL1, HRX, HTRX, TRX1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03164 |
-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 conditions | pH: 5.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: iNITIAL STRUCTURE CALCULATION USING TORSION ANGLE DYNAMICS IN DYANA FOLLOWED BY REFINEMENT IN AMBER USING SIMULATED ANNEALING AND ENERGY MINIMIZATION IN VACUO AND GENERALIZED BORN POTENTIAL | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: lowest energy and lowest distance and angle violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |