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- PDB-1wtb: Complex structure of the C-terminal RNA-binding domain of hnRNP D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wtb | ||||||
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Title | Complex structure of the C-terminal RNA-binding domain of hnRNP D (AUF1) with telomere DNA | ||||||
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![]() | TRANSCRIPTION/DNA / RNA-binding domain / DNA-binding domain / RRM / hnRNP D / AUF1 / Telomere / Complex / structural genomics / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / mCRD-mediated mRNA stability complex / positive regulation of telomerase RNA reverse transcriptase activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization ...hepatocyte dedifferentiation / cellular response to putrescine / circadian regulation of translation / response to rapamycin / mCRD-mediated mRNA stability complex / positive regulation of telomerase RNA reverse transcriptase activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / response to sodium phosphate / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / positive regulation of cytoplasmic translation / RNA catabolic process / regulation of telomere maintenance / telomeric DNA binding / minor groove of adenine-thymine-rich DNA binding / positive regulation of telomere capping / Processing of Capped Intron-Containing Pre-mRNA / cellular response to nitric oxide / RNA processing / response to electrical stimulus / mRNA Splicing - Major Pathway / cerebellum development / liver development / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of translation / cellular response to estradiol stimulus / cellular response to amino acid stimulus / mRNA transcription by RNA polymerase II / regulation of circadian rhythm / histone deacetylase binding / response to calcium ion / regulation of gene expression / postsynaptic density / ribonucleoprotein complex / negative regulation of gene expression / glutamatergic synapse / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Enokizono, Y. / Konishi, Y. / Nagata, K. / Ouhashi, K. / Uesugi, S. / Ishikawa, F. / Katahira, M. | ||||||
![]() | ![]() Title: Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D Authors: Enokizono, Y. / Konishi, Y. / Nagata, K. / Ouhashi, K. / Uesugi, S. / Ishikawa, F. / Katahira, M. #1: ![]() Title: Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA Authors: Katahira, M. / Miyanoiri, Y. / Enokizono, Y. / Matsuda, G. / Nagata, T. / Ishikawa, F. / Uesugi, S. #2: ![]() Title: Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0 Authors: Nagata, T. / Kurihara, Y. / Matsuda, G. / Saeki, J. / Kohno, T. / Yanagida, Y. / Ishikawa, F. / Uesugi, S. / Katahira, M. #3: Journal: Mol.Cell.Biol. / Year: 1993 Title: Nuclear proteins that bind the pre-mRNA 3' splice site sequence r(UUAG/G) and the human telomeric DNA sequence d(TTAGGG)n Authors: Ishikawa, F. / Matunis, M.J. / Dreyfuss, G. / Cech, T.R. | ||||||
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 554.6 KB | Display | ![]() |
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PDB format | ![]() | 460.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 347.8 KB | Display | ![]() |
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Full document | ![]() | 595.2 KB | Display | |
Data in XML | ![]() | 89.9 KB | Display | |
Data in CIF | ![]() | 120.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 1230.854 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 9103.628 Da / Num. of mol.: 1 / Fragment: C-terminal RNA-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 100mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 288 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |