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- PDB-2n3f: Solution structure of both dsRBDs of DRB4 along with linker (viz.... -

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Basic information

Entry
Database: PDB / ID: 2n3f
TitleSolution structure of both dsRBDs of DRB4 along with linker (viz. DRB4(1-153))
ComponentsDouble-stranded RNA-binding protein 4
KeywordsRNA BINDING PROTEIN / RNAi
Function / homology
Function and homology information


ta-siRNA processing / RNAi-mediated antiviral immune response / miRNA processing / double-stranded RNA binding / defense response to virus / nucleus
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 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
Double-stranded RNA-binding protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsDeshmukh, M. / Chiliveri, S.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.
Authors: Chiliveri, S.C. / Aute, R. / Rai, U. / Deshmukh, M.V.
History
DepositionMay 29, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-stranded RNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)16,6191
Polymers16,6191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
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 4 / dsRNA-binding protein 4 / AtDRB4


Mass: 16618.721 Da / Num. of mol.: 1 / Fragment: DRBM domains 1 and 2, residues 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DBR4, At3g62800, F26K9.230 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H1D4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HN(CA)CO
1423D HNCA
1523D HN(CO)CA
1623D HN(CA)CB
1723D HN(COCA)CB
1822D 1H-13C HSQC
1923D H(CCO)NH-TOCSY
11023D (H)C(CO)NH-TOCSY
11123D (H)CCH-TOCSY
11223D HNHA
11372D 1H-13C HSQC
11432D 1H-13C HSQC
11543D 1H-13C NOESY
11652D 1H-15N HSQC
11752D 1H-1H NOESY
11832D 1H-15N HSQC
11962D 1H-15N HSQC
12013D 1H-15N NOESY
12123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM [U-100% 15N] DRB4(1-153), 90% H2O/10% D2O90% H2O/10% D2O
2500 uM [U-100% 13C; U-100% 15N] DRB4(1-153), 90% H2O/10% D2O90% H2O/10% D2O
3250 uM [U-100% 15N] DRB4(1-153), 90% H2O/10% D2O90% H2O/10% D2O
4500 uM [U-100% 15N] DRB4(1-153), 500 uM U-13C,1H MeOnly Ile, Leu, Val (rest 12C,1H); U-15N DRB4(1-153), 100% D2O100% D2O
5500 uM [U-100% 15N] DRB4(1-153), 500 uM U-13C,1H MeOnly Ile, Leu, Val (rest 12C,1H); U-15N DRB4(1-153), 100% D2O100% D2O
6500 uM [U-100% 13C; U-100% 15N] DRB4(1-153), filamentous virus, 18mg/mL, 90% H2O/10% D2O90% H2O/10% D2O
7500 uM [U-10% 13C] DRB4(1-153), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMDRB4(1-153)-1[U-100% 15N]1
500 uMDRB4(1-153)-2[U-100% 13C; U-100% 15N]2
250 uMDRB4(1-153)-3[U-100% 15N]3
500 uMDRB4(1-153)-4[U-100% 15N]4
500 uMDRB4(1-153)-5U-13C,1H MeOnly Ile, Leu, Val (rest 12C,1H); U-15N4
500 uMDRB4(1-153)-6[U-100% 15N]5
500 uMDRB4(1-153)-7U-13C,1H MeOnly Ile, Leu, Val (rest 12C,1H); U-15N5
500 uMDRB4(1-153)-8[U-100% 13C; U-100% 15N]6
500 uMDRB4(1-153)-9[U-10% 13C]7
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1.6Bruker Biospincollection
TopSpin2.1.6Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
SparkyGoddarddata analysis
SparkyGoddardstructure solution
SparkySchwieters, Kuszewski, Tjandra and Cloredata analysis
SparkySchwieters, Kuszewski, Tjandra and Clorestructure solution
SparkyGoddarddata analysis
SparkyGoddardstructure solution
SparkySchwieters, Kuszewski, Tjandra and Cloredata analysis
SparkySchwieters, Kuszewski, Tjandra and Clorestructure solution
ProcheckNMR3.5.4Laskowski and MacArthurstructure validation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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