[English] 日本語
Yorodumi- PDB-5xv8: Solution structure of the complex between UVSSA acidic region and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xv8 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the complex between UVSSA acidic region and TFIIH p62 PH domain | ||||||
Components |
| ||||||
Keywords | NUCLEAR PROTEIN / DNA repair factor / general transcription factor / nucleotide excision repair / transcription-coupled repair | ||||||
Function / homology | Function and homology information transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping ...transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 complex binding / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / hormone-mediated signaling pathway / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome / transcription by RNA polymerase II / protein ubiquitination / DNA repair / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Authors | Okuda, M. / Nishimura, Y. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways Authors: Okuda, M. / Nakazawa, Y. / Guo, C. / Ogi, T. / Nishimura, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xv8.cif.gz | 949.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xv8.ent.gz | 795.6 KB | Display | PDB format |
PDBx/mmJSON format | 5xv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xv8_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xv8_full_validation.pdf.gz | 720.7 KB | Display | |
Data in XML | 5xv8_validation.xml.gz | 74.2 KB | Display | |
Data in CIF | 5xv8_validation.cif.gz | 96 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/5xv8 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xv8 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 5507.810 Da / Num. of mol.: 1 / Fragment: UNP residues 390-434 Source method: isolated from a genetically manipulated source Details: The three amino acids (GSM) at the N terminus do not derive from UVSSA. Source: (gene. exp.) Homo sapiens (human) / Gene: UVSSA, KIAA1530 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YD98 |
---|---|
#2: Protein | Mass: 12450.445 Da / Num. of mol.: 1 / Fragment: UNP residues 2-108 Source method: isolated from a genetically manipulated source Details: The two amino acids (GS) at the N terminus do not derive from TFIIH p62. Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32780 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| ||||||||||||||||||||||||||||||||||||
Sample conditions | Details: 20 mM KPB (pH6.8), 5mM d-DTT / Ionic strength: 20 mM / Label: 1 / pH: 6.80 / Pressure: 760 mmHg / Temperature: 305 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 6 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |