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Yorodumi- PDB-2lef: LEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lef | |||||||||
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Title | LEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 STRUCTURES | |||||||||
Components |
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Keywords | GENE REGULATION/DNA / LEF1 / HMG / TCR-A / TRANSCRIPTION FACTOR / DNA BINDING / DNA BENDING / COMPLEX (HMG DOMAIN-DNA) / GENE REGULATION-DNA COMPLEX | |||||||||
Function / homology | Function and homology information Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / : / RUNX3 regulates WNT signaling / negative regulation of interleukin-4 production / positive regulation of cell cycle process ...Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / : / RUNX3 regulates WNT signaling / negative regulation of interleukin-4 production / positive regulation of cell cycle process / positive regulation of granulocyte differentiation / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / formation of radial glial scaffolds / negative regulation of apoptotic process in bone marrow cell / neutrophil differentiation / armadillo repeat domain binding / negative regulation of striated muscle tissue development / Formation of the beta-catenin:TCF transactivating complex / Deactivation of the beta-catenin transactivating complex / T-helper 1 cell differentiation / positive regulation of cell proliferation in bone marrow / odontoblast differentiation / Ca2+ pathway / apoptotic process involved in morphogenesis / secondary palate development / cell development / beta-catenin-TCF complex / regulation of cell-cell adhesion / positive regulation of gamma-delta T cell differentiation / apoptotic process involved in blood vessel morphogenesis / T cell receptor V(D)J recombination / gamma-catenin binding / positive regulation of odontoblast differentiation / forebrain radial glial cell differentiation / positive regulation of chondrocyte proliferation / dentate gyrus development / mammary gland development / vasculature development / C2H2 zinc finger domain binding / transcription regulator inhibitor activity / positive regulation by host of viral transcription / embryonic limb morphogenesis / face morphogenesis / regulation of Wnt signaling pathway / sprouting angiogenesis / epithelial cell apoptotic process / DNA binding, bending / alpha-beta T cell differentiation / tongue development / branching involved in blood vessel morphogenesis / B cell proliferation / cellular response to cytokine stimulus / odontogenesis of dentin-containing tooth / positive regulation of Wnt signaling pathway / regulation of neurogenesis / canonical Wnt signaling pathway / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / BMP signaling pathway / cis-regulatory region sequence-specific DNA binding / somitogenesis / protein localization to chromatin / cellular response to interleukin-4 / cell chemotaxis / transcription corepressor binding / nuclear estrogen receptor binding / protein-DNA complex / hippocampus development / positive regulation of cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / beta-catenin binding / osteoblast differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / sensory perception of taste / histone deacetylase binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / histone binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | SOLUTION NMR / DG IN TORSION SPACE (DIANA), DYNAMICAL SIMULATED ANNEALING | |||||||||
Authors | Li, X. / Love, J.J. / Case, D.A. / Wright, P.E. | |||||||||
Citation | Journal: Nature / Year: 1995 Title: Structural basis for DNA bending by the architectural transcription factor LEF-1. Authors: Love, J.J. / Li, X. / Case, D.A. / Giese, K. / Grosschedl, R. / 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 | 2lef.cif.gz | 570 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lef.ent.gz | 470 KB | Display | PDB format |
PDBx/mmJSON format | 2lef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/2lef ftp://data.pdbj.org/pub/pdb/validation_reports/le/2lef | 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: DNA chain | Mass: 4504.936 Da / Num. of mol.: 1 / Fragment: LEF-1 BINDING SITE / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4674.046 Da / Num. of mol.: 1 / Fragment: LEF-1 BINDING SITE / Source method: obtained synthetically |
#3: Protein | Mass: 10403.220 Da / Num. of mol.: 1 / Fragment: HMG / Mutation: CHAIN A, C25S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BL21 (DE3) / Cell: PRE-B AND T LYMPHOCYTE / Gene: LEF1 / Plasmid: PET-21A / Species (production host): Escherichia coli / Gene (production host): LEF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P27782 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: PRESSURE: 1 ATM SOLVENT SYSTEM: 90%H2O/10%D2O, |
-Sample preparation
Sample conditions | Ionic strength: 10 mM KCL / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DG IN TORSION SPACE (DIANA), DYNAMICAL SIMULATED ANNEALING Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE | |||||||||||||||
NMR ensemble | Conformer selection criteria: CONSTRAINTS VIOLATION, AMBER ENERGIES Conformers calculated total number: 28 / Conformers submitted total number: 12 |