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- PDB-9gdw: RNA binding domain of Turnip crinkle virus p38, p38R -

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Basic information

Entry
Database: PDB / ID: 9gdw
TitleRNA binding domain of Turnip crinkle virus p38, p38R
ComponentsCapsid protein
KeywordsRNA BINDING PROTEIN / RNA interference (RNAi) / viral suppressor of RNA silencing (VSR) / plant virus / Turnip crinkle virus / dsRNA / siRNA / miRNA
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / symbiont-mediated suppression of host innate immune response / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesTurnip crinkle virus
MethodSOLUTION NMR / simulated annealing
AuthorsWeininger, U. / Golbik, R. / Thondorf, I. / Behrens, S.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: RNA binding domain of Turnip crinkle virus p38, p38R
Authors: Weininger, U. / Golbik, R. / Thondorf, I. / Behrens, S.E.
History
DepositionAug 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)5,1871
Polymers5,1871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Capsid protein / Coat protein / p38


Mass: 5187.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip crinkle virus / Gene: ORF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P06663
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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D 1H-15N TOCSY
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 bar / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRViewJJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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