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Open data
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Basic information
Entry | Database: PDB / ID: 2lts | ||||||
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Title | Solution structure of RDE-4(150-235) | ||||||
![]() | Protein RDE-4 | ||||||
![]() | RNA BINDING PROTEIN / RDE-4 / dsRBD2 / RNAi / RDE-4DC | ||||||
Function / homology | ![]() MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA binding / siRNA processing / RISC complex / double-stranded RNA binding ...MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA binding / siRNA processing / RISC complex / double-stranded RNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein homodimerization activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Deshmukh, M. / Chiliveri, S. | ||||||
![]() | ![]() Title: Structure of RDE-4 dsRBDs and mutational studies provide insights into dsRNA recognition in the Caenorhabditis elegans RNAi pathway. Authors: Chiliveri, S.C. / Deshmukh, M.V. #1: Journal: Biomol.Nmr Assign. / Year: 2011 Title: Backbone and sidechain methyl Ile (delta1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans. Authors: Chiliveri, S.C. / Kumar, S. / Marelli, U.K. / Deshmukh, M.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.2 KB | Display | ![]() |
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PDB format | ![]() | 231.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 624.5 KB | Display | ![]() |
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Full document | ![]() | 768.9 KB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 44.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ltrC C: citing same article ( |
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Similar 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: Protein | Mass: 27860.629 Da / Num. of mol.: 1 / Fragment: dsRBD2 (UniProt residues 150-235) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Solution structure of RDE-4(150-235) containing linker and dsRBD2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE PROTEIN USED IN THIS STUDY (UNP RESIDUES 1-243) IS A FRAGMENT OF RDE-4, AN RNAI INITIATOR PROTEIN IN C. ELEGANS. IT CONSISTS OF FOUR REGIONS, WHICH ARE THE N-TERMINAL REGION (1-43), ...Details: THE PROTEIN USED IN THIS STUDY (UNP RESIDUES 1-243) IS A FRAGMENT OF RDE-4, AN RNAI INITIATOR PROTEIN IN C. ELEGANS. IT CONSISTS OF FOUR REGIONS, WHICH ARE THE N-TERMINAL REGION (1-43), DSRBD1 (44-107), LINKER (108-168), AND DSRBD2 (169-235). IN THE COURSE OF ASSIGNMENTS AND STRUCTURE CALCULATION, A PART OF THE LINKER (RESIDUES 126-149) IS FOUND TO BE HIGHLY FLEXIBLE. NO SPATIAL INTER-DOMAIN CONTACTS WERE OBSERVED BETWEEN THE TWO DSRBDS. THEREFORE, SOLUTION STRUCTURES OF DSRBD1 AND DSRBD2 WERE CALCULATED SEPARATELY. FOR 2LTR, RIGID PART OF N-TERMINAL REGION (32-43), DSRBD1 (44-107) AND LINKER REGION (108-136) WERE USED TO CALCULATE THE FINAL STRUCTURES, WHEREAS FOR 2LTS, RIGID PART OF THE LINKER (150-168) AND DSRBD2 (169-235) WERE CHOSEN FOR THE CALCULATION OF THE FINAL STRUCTURES. THE RELATIVE ORIENTATION BETWEEN TWO STRUCTURES COULD NOT BE DETERMINED DUE TO THE FLEXIBLE NATURE OF THE LINKER. | |||||||||||||||||||||
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: 10 |