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- PDB-9jvc: Solution Structure of DRB2 dsRBD1 -

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Basic information

Entry
Database: PDB / ID: 9jvc
TitleSolution Structure of DRB2 dsRBD1
ComponentsDouble-stranded RNA-binding protein 2
KeywordsRNA BINDING PROTEIN / DRB2 / DRB1 / DCL1 / A. thaliana / RNAi / Stress response / miRNA
Function / homology
Function and homology information


miRNA processing / double-stranded RNA binding / cytoplasm
Similarity search - Function
AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
Double-stranded RNA-binding protein 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPatra, D. / Rai, U. / Deshmukh, M.V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)MLP0161 India
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Conformational Plasticity in dsRNA-Binding Domains Drives Functional Divergence in RNA Recognition.
Authors: Patra, D. / Paul, J. / Rai, U. / P S, A. / Deshmukh, M.V.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Double-stranded RNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)8,5101
Polymers8,5101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable, NMR relaxation study, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Double-stranded RNA-binding protein 2 / dsRNA-binding protein 2 / AtDRB2


Mass: 8510.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: Root Meristem, / Gene: DRB2 / Organ: Roots, Flowers, Leaves / Plasmid: pET30a / Details (production host): Kan resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SKN2
Has protein modificationN

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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
123isotropic12D 1H-13C HSQC
133isotropic13D HNCO
143isotropic13D HN(CA)CO
153isotropic13D HN(COCA)CB
1133isotropic13D HN(CA)CB
1123isotropic13D (H)CCH-TOCSY
1113isotropic13D H(CCO)NH TOCSY
1103isotropic13D (H)C(CO)NH TOCSY
193isotropic13D HNCA
183isotropic13D 1H-13C NOESY aliphatic
173isotropic13D 1H-15N NOESY
1143isotropic13D HNHA
1162anisotropic12D 1H-15N HSQC
1152anisotropic12D 1H-15N HSQC TROSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1200 uM [U-98% 15N] DRB2 dsRBD1, 90% H2O/10% D2OU 15N15N90% H2O/10% D2O
filamentous virus2440 uM [U-13C; U-15N] DRB2 dsRBD1, 90% H2O/10% D2OU 15Nalignment90% H2O/10% D2O
solution3500 uM [U-13C; U-15N] DRB2 dsRBD1, 90% H2O/10% D2OU 15N13C 15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMDRB2 dsRBD1[U-98% 15N]1
440 uMDRB2 dsRBD1[U-13C; U-15N]2
500 uMDRB2 dsRBD1[U-13C; U-15N]3
Sample conditionsDetails: 50 mM KPhophate buffer (pH 6.8), 50 mM NaCl, 50 mM Na2SO4, 4 mM DTT
Ionic strength: 150 mM / Label: 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospincollection
TopSpin4Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
NMRtistKlukowski, Riek and Guntertdata analysis
TALOS-NCornilescu, Delaglio and Baxchemical shift calculation
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 9
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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