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- PDB-2kou: DICER LIKE protein -

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Basic information

Entry
Database: PDB / ID: 2kou
TitleDICER LIKE protein
ComponentsDicer-like protein 4
KeywordsHYDROLASE / DICER-LIKE protein / ATP-binding / Endonuclease / Helicase / Nuclease / Nucleotide-binding / Nucleus / RNA-binding / RNA-mediated gene silencing
Function / homology
Function and homology information


vegetative phase change / lsiRNA processing / RNAi-mediated antiviral immunity against RNA virus / polarity specification of adaxial/abaxial axis / : / ta-siRNA processing / maintenance of shoot apical meristem identity / RNAi-mediated antiviral immune response / reproductive structure development / ribonuclease III activity ...vegetative phase change / lsiRNA processing / RNAi-mediated antiviral immunity against RNA virus / polarity specification of adaxial/abaxial axis / : / ta-siRNA processing / maintenance of shoot apical meristem identity / RNAi-mediated antiviral immune response / reproductive structure development / ribonuclease III activity / siRNA processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / helicase activity / DNA-templated transcription termination / defense response to virus / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Dicer dimerisation domain / Dicer dimerisation domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain ...Dicer dimerisation domain / Dicer dimerisation domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dicer-like protein 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsQin, H. / Song, J. / Yuan, Y.A.
CitationJournal: Rna / Year: 2010
Title: Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction
Authors: Qin, H. / Chen, F. / Huan, X. / Machida, S. / Song, J. / Yuan, Y.A.
History
DepositionSep 30, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dicer-like protein 4


Theoretical massNumber of molelcules
Total (without water)11,3271
Polymers11,3271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Dicer-like protein 4


Mass: 11326.758 Da / Num. of mol.: 1 / Fragment: residue in UNP 629-730 / Mutation: L9M, L10M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DCL4, At5g20320, F5O24.210 / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: P84634, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D 1H-15N NOESY
1413D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] DCL4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: DCL4 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.02 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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