[English] 日本語
Yorodumi- PDB-5urn: NMR structure of the complex between the PH domain of the Tfb1 su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5urn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65 | |||||||||
Components |
| |||||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR TFIIH / TRANSACTIVATION DOMAIN / NUCLEAR FACTOR KAPPA-B / TRANSCRIPTIONAL ACTIVATION / P62/TFB1 SUBUNIT | |||||||||
Function / homology | Function and homology information 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 / Regulated proteolysis of p75NTR ...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 / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / phosphatidylinositol-3-phosphate binding / SUMOylation of immune response proteins / negative regulation of protein sumoylation / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / Interleukin-1 processing / cellular response to interleukin-6 / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / Regulation of NFE2L2 gene expression / toll-like receptor 4 signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / cellular response to hepatocyte growth factor stimulus / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 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 / positive regulation of T cell receptor signaling pathway / response to cobalamin / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / phosphate ion binding / non-canonical NF-kappaB signal transduction / Gap-filling DNA repair synthesis and ligation in TC-NER / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / canonical NF-kappaB signal transduction / transcription by RNA polymerase I / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / negative regulation of miRNA transcription / response to progesterone / liver development / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / negative regulation of extrinsic apoptotic signaling pathway / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / animal organ morphogenesis / protein catabolic process / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / negative regulation of protein catabolic process / transcription coactivator binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Lecoq, L. / Omichinski, J.G. / Raiola, L. / Cyr, N. / Chabot, P. / Arseneault, G. / Legault, P. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5urn.cif.gz | 886.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5urn.ent.gz | 744.3 KB | Display | PDB format |
PDBx/mmJSON format | 5urn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/5urn ftp://data.pdbj.org/pub/pdb/validation_reports/ur/5urn | HTTPS FTP |
---|
-Related structure data
Related structure data | 5u4kC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-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 (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TFB1, YDR311W, D9740.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32776 |
---|---|
#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.) Homo sapiens (human) / Gene: RELA, NFKB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04206 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||
Sample conditions | Ionic strength: 0 mM / Label: Condition1 / pH: 6.5 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |