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Open data
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Basic information
Entry | Database: PDB / ID: 2ltr | ||||||
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Title | Solution structure of RDE-4(32-136) | ||||||
![]() | Protein RDE-4 | ||||||
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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 processing / siRNA binding / RISC complex / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.4 KB | Display | ![]() |
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PDB format | ![]() | 281.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2ltsC C: citing same article ( |
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Similar structure data | |
Other databases |
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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: dsRBD1 (UniProt residues 32-136) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() Details: Solution structure of RDE-4(32-136) containing N-terminal helix, dsRBD1 and part of the linker | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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![]() |
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Processing
NMR software |
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Refinement | Method: ![]() 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 |