+Open data
-Basic information
Entry | Database: PDB / ID: 8kfp | ||||||
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Title | Solution structure of Drosophila melanogaster R2D2 dsRBD1 | ||||||
Components | R2D2 | ||||||
Keywords | RNA BINDING PROTEIN / RNAi / siRNA / Dicer-2 / dsRNA | ||||||
Function / homology | Function and homology information regulatory ncRNA processing / follicle cell of egg chamber stalk formation / regulation of regulatory ncRNA processing / RISC-loading complex / RISC complex assembly / siRNA binding / siRNA processing / RISC complex / double-stranded RNA binding / defense response to virus ...regulatory ncRNA processing / follicle cell of egg chamber stalk formation / regulation of regulatory ncRNA processing / RISC-loading complex / RISC complex assembly / siRNA binding / siRNA processing / RISC complex / double-stranded RNA binding / defense response to virus / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | MODEL GENERATED BY ROSETTA VERSION 2021.16+release.8ee4f02 | ||||||
Authors | Aute, R. / Deshmukh, M.V. | ||||||
Funding support | India, 1items
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Citation | Journal: Biophys.Chem. / Year: 2024 Title: Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Authors: Aute, R. / Waghela, N. / Deshmukh, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kfp.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kfp.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 8kfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kfp_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 8kfp_full_validation.pdf.gz | 558.1 KB | Display | |
Data in XML | 8kfp_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 8kfp_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/8kfp ftp://data.pdbj.org/pub/pdb/validation_reports/kf/8kfp | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11311.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: dsRBD1 of R2D2 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: r2d2 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2Q0L0 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 150 mM / Label: conditions _1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 5000 / Conformers submitted total number: 10 |