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- PDB-9jmt: DRB3 dsRBD1 (i.e., DRB3(1-75)) -

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Basic information

Entry
Database: PDB / ID: 9jmt
TitleDRB3 dsRBD1 (i.e., DRB3(1-75))
ComponentsDouble-stranded RNA-binding protein 3
KeywordsRNA BINDING PROTEIN / A. thaliana / RNAi / DCL3 / dsRBD
Function / homologyAtDRB-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 / double-stranded RNA binding / Double-stranded RNA-binding protein 3
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPaul, J. / 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
DepositionSep 21, 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 3


Theoretical massNumber of molelcules
Total (without water)9,3521
Polymers9,3521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable, NMR relaxation study
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 3 / dsRNA-binding protein 3 / AtDRB3


Mass: 9352.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: shoot apical meristem / Gene: At3g26932 / Organ: young flowers and young leaves / Plasmid: pET30a-DRB3D1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LJF5
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
122isotropic12D 1H-13C HSQC
132isotropic13D HNCO
142isotropic13D HN(CA)CO
152isotropic13D HN(COCA)CB
1112isotropic13D HN(CA)CB
1102isotropic13D (H)CCH-TOCSY
192isotropic13D H(CCO)NH TOCSY
182isotropic13D (H)C(CCO)NH TOCSY
172isotropic13D 1H-15N NOESY HSQC
162isotropic13D 1H-13C NOESY HSQC aliphatic
1121anisotropic12D 1H-15N IPAP HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1200 uM [U-15N] DRB3D1, 90% H2O/10% D2O15N15N90% H2O/10% D2O
solution2550 uM [U-13C; U-15N] DRB3D1, 90% H2O/10% D2O15N 13C13C 15N90% H2O/10% D2O
bicelle3300 uM [U-15N] DRB3D1, 90% H2O/10% D2O15N15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMDRB3D1[U-15N]1
550 uMDRB3D1[U-13C; U-15N]2
300 uMDRB3D1[U-15N]3
Sample conditionsDetails: 50 mM Pot Phosphate (pH 6.8), 50 mM NaCl, 50 mM Na2SO4, 2 mM DTT
Ionic strength: 150 mM / Label: K Phosph buffer / 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
TopSpin4Bruker Biospindata analysis
CARA1.9.1Keller and Wuthrichpeak picking
CARA1.9.1Keller and Wuthrichchemical shift assignment
TALOS-NCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIH3.5Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3.5Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 2
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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