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- PDB-5npg: Solution structure of Drosophila melanogaster Loquacious dsRBD1 -

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Basic information

Entry
Database: PDB / ID: 5npg
TitleSolution structure of Drosophila melanogaster Loquacious dsRBD1
ComponentsLoquacious, isoform F
KeywordsRNA BINDING PROTEIN / dsRBD / RNA interference / siRNA
Function / homology
Function and homology information


regulatory ncRNA processing / female germ-line stem cell asymmetric division / regulation of regulatory ncRNA processing / dosage compensation by hyperactivation of X chromosome / germ-line stem cell population maintenance / miRNA metabolic process / pre-miRNA processing / siRNA processing / central nervous system development / double-stranded RNA binding / cytoplasm
Similarity search - Function
Staufen, C-terminal / Staufen C-terminal domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Loquacious, isoform F
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / Rasrec
AuthorsTants, J.-N. / Fesser, S. / Kern, T. / Stehle, R. / Geerlof, A. / Wunderlich, C. / Hartlmuller, C. / Boettcher, R. / Kunzelmann, S. / Lange, O. ...Tants, J.-N. / Fesser, S. / Kern, T. / Stehle, R. / Geerlof, A. / Wunderlich, C. / Hartlmuller, C. / Boettcher, R. / Kunzelmann, S. / Lange, O. / Kreutz, C. / Foerstemann, K. / Sattler, M.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference.
Authors: Tants, J.N. / Fesser, S. / Kern, T. / Stehle, R. / Geerlof, A. / Wunderlich, C. / Juen, M. / Hartlmuller, C. / Bottcher, R. / Kunzelmann, S. / Lange, O. / Kreutz, C. / Forstemann, K. / Sattler, M.
History
DepositionApr 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.5May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Loquacious, isoform F


Theoretical massNumber of molelcules
Total (without water)9,1061
Polymers9,1061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4480 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 5000Rosetta score
RepresentativeModel #10

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Components

#1: Protein Loquacious, isoform F


Mass: 9105.568 Da / Num. of mol.: 1 / Fragment: UNP residues 129-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: loqs, Dmel\CG6866, dRax, loq, LOQS, Loqs, R3D1, r3d1, R3D1-L, R3D1-S, TRBP, CG6866, Dmel_CG6866
Production host: Escherichia coli (E. coli) / References: UniProt: X2J5X6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution / Contents: 2 g/L [U-13C; U-15N] dsRBD1, 90% H2O/10% D2O / Label: dsRBD1_15N13C / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 g/L / Component: dsRBD1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 500 NaCl, 20 PO4 mM / Label: assignment / pH: 6.5 / Pressure: 101325 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

SoftwareName: CS-ROSETTA / Classification: refinement
NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: Rasrec / Software ordinal: 3
NMR representativeSelection criteria: 0
NMR ensembleConformer selection criteria: Rosetta score / Conformers calculated total number: 5000 / Conformers submitted total number: 10 / Representative conformer: 1

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