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Yorodumi- PDB-2n23: NMR structure of the complex between the PH domain of the Tfb1 su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2n23 | ||||||
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Title | NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1) | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor TFIIH / Transactivation domain / Erythroid Kr ppel-like factor 1 / Transcriptional activation / p62/Tfb1 subunit | ||||||
Function / homology | Function and homology information cellular response to peptide / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex ...cellular response to peptide / phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / maternal process involved in female pregnancy / transcription by RNA polymerase I / erythrocyte differentiation / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Lecoq, L. / Morse, T. / Raiola, L. / Arseneault, G. / Omichinski, J. | ||||||
Citation | Journal: To be Published Title: Structural Characterization of the Complex between the N-terminal Transactivation Domain of EKLF and the p62/Tfb1 subunit of TFIIH Authors: Morse, T. / Lecoq, L. / Raiola, L. / Arseneault, G. / Omichinski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n23.cif.gz | 910.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n23.ent.gz | 802.4 KB | Display | PDB format |
PDBx/mmJSON format | 2n23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/2n23 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/2n23 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12903.701 Da / Num. of mol.: 1 / Fragment: Pleckstrin homology domain, UNP residues 2-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32776 |
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#2: Protein/peptide | Mass: 2359.483 Da / Num. of mol.: 1 / Fragment: Transactivation Domain 1, UNP residues 22-40 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLF1, EKLF / Production host: Escherichia coli (E. coli) / References: UniProt: Q13351 |
-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: 0 / pH: 6.5 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CNS / Classification: refinement |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 |
NMR constraints | NOE constraints total: 2737 / NOE intraresidue total count: 1453 / NOE long range total count: 540 / NOE medium range total count: 2015 / NOE sequential total count: 486 / Protein phi angle constraints total count: 119 / Protein psi angle constraints total count: 119 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 260 / Conformers submitted total number: 20 |