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- PDB-5urn: NMR structure of the complex between the PH domain of the Tfb1 su... -
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Basic information
Entry | Database: PDB / ID: 5urn | |||||||||
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Title | NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65 | |||||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION FACTOR TFIIH / TRANSACTIVATION DOMAIN / NUCLEAR FACTOR KAPPA-B / TRANSCRIPTIONAL ACTIVATION / P62/TFB1 SUBUNIT | |||||||||
Function / homology | ![]() phosphatidylinositol-5-phosphate binding / acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / nucleotide-excision repair factor 3 complex / cellular response to peptidoglycan / ankyrin repeat binding ...phosphatidylinositol-5-phosphate binding / acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / nucleotide-excision repair factor 3 complex / cellular response to peptidoglycan / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / defense response to tumor cell / phosphatidylinositol-3-phosphate binding / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / Interleukin-1 processing / transcription factor TFIIH core complex / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / transcription factor TFIIH holo complex / cellular response to angiotensin / response to UV-B / NF-kappaB complex / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / 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 / response to cobalamin / Formation of TC-NER Pre-Incision Complex / positive regulation of T cell receptor signaling pathway / RNA Polymerase I Promoter Escape / phosphate ion binding / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to lipoteichoic acid / transcription by RNA polymerase I / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / general transcription initiation factor binding / neuropeptide signaling pathway / Dual incision in TC-NER / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / cellular defense response / Purinergic signaling in leishmaniasis infection / canonical NF-kappaB signal transduction / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / response to muscle stretch / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / response to interleukin-1 / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / nucleotide-excision repair / Dectin-1 mediated noncanonical NF-kB signaling / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / Activation of NF-kappaB in B cells / peptide binding / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / protein catabolic process / negative regulation of protein catabolic process / chromatin DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Lecoq, L. / Omichinski, J.G. / Raiola, L. / Cyr, N. / Chabot, P. / Arseneault, G. / Legault, P. | |||||||||
![]() | ![]() Title: Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kappa B and transcription regulatory factors. Authors: Lecoq, L. / Raiola, L. / Chabot, P.R. / Cyr, N. / Arseneault, G. / Legault, P. / Omichinski, J.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 890.3 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5u4kC C: citing same article ( |
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Similar structure data | |
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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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 3378.591 Da / Num. of mol.: 1 / Fragment: TRANSACTIVATION DOMAIN 1, UNP RESIDUES 521-551 / Mutation: L523Y Source method: isolated from a genetically manipulated source Details: The first GS residues come from a purification TAG. Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | Ionic strength: 0 mM / Label: Condition1 / pH: 6.5 / Pressure: AMBIENT / 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: SIDECHAINS OPTIMIZATION WITH YASARA | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 260 / Conformers submitted total number: 20 |