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Yorodumi- PDB-1t2s: Structural basis for 3' end recognition of nucleic acids by the D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t2s | ||||||
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Title | Structural basis for 3' end recognition of nucleic acids by the Drosophila Argonaute 2 PAZ domain | ||||||
Components |
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Keywords | nucleic acid binding protein/dna / nucleic acid binding protein / dna / nucleic acid binding protein-dna COMPLEX | ||||||
Function / homology | Function and homology information syncytial nuclear migration / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated retrotransposon silencing by heterochromatin formation / RNAi-mediated antiviral immune response / RNA endonuclease activity, producing 5'-phosphomonoesters / MicroRNA (miRNA) biogenesis / pole cell formation / Small interfering RNA (siRNA) biogenesis / endoribonuclease activity, cleaving siRNA-paired mRNA ...syncytial nuclear migration / Post-transcriptional silencing by small RNAs / cellularization / siRNA-mediated retrotransposon silencing by heterochromatin formation / RNAi-mediated antiviral immune response / RNA endonuclease activity, producing 5'-phosphomonoesters / MicroRNA (miRNA) biogenesis / pole cell formation / Small interfering RNA (siRNA) biogenesis / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / segment polarity determination / neuronal ribonucleoprotein granule / dsRNA transport / dosage compensation by hyperactivation of X chromosome / messenger ribonucleoprotein complex / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / RISC complex assembly / siRNA processing / siRNA binding / RISC complex / negative regulation of viral genome replication / RNA endonuclease activity / cellular response to virus / defense response to virus / single-stranded RNA binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING | ||||||
Authors | Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Nucleic acid 3'-end recognition by the Argonaute2 PAZ domain. Authors: Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M. #1: Journal: NATURE / Year: 2003 Title: STRUCTURE AND NUCLEIC-ACID BINDING OF THE DROSOPHILA ARGONAUTE 2 PAZ DOMAIN Authors: Lingel, A. / Simon, B. / Izaurralde, E. / Sattler, M. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES 1-4 IN THE CONSTRUCT USED FOR THE STRUCTURE DETERMINATION ARE FROM THE EXPRESSION VECTOR. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t2s.cif.gz | 438.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t2s.ent.gz | 381.1 KB | Display | PDB format |
PDBx/mmJSON format | 1t2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/1t2s ftp://data.pdbj.org/pub/pdb/validation_reports/t2/1t2s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 1439.988 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 13928.974 Da / Num. of mol.: 1 / Fragment: paz domain, residues 605-723 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PETM60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VUQ5 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: STRUCTURAL RESTRAINTS WERE DERIVED FROM 13C AND 15N-EDITED AND EDITED FILTERED NOESY EXPERIMENTS |
-Sample preparation
Details | Contents: 0.2-1 MM 15N OR 15N,13C-LABELED PROTEIN, 0.1-2.5 MM UNLABELED DNA, 50 MM SODIUM PHOSPHATE BUFFER, 0.2 MM DTT |
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Sample conditions | pH: 6.8 / Pressure: 1 atm / Temperature: 295 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1 Details: THE EXPERIMENTALLY DETERMINED DISTANCE RESTRAINTS WERE APPLIED IN A MIXED TORSION AND CARTESIA DYNAMICS SIMULATED ANNEALING PROTOCOL. THE FINAL STRUCTURE ENSEMBLE WAS REFINED IN A SHELL OF WATER MOLECULES. | ||||||||||||
NMR representative | Selection criteria: lowest energies | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGIES / Conformers calculated total number: 150 / Conformers submitted total number: 10 |