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- PDB-2lup: RDC refined solution structure of double-stranded RNA binding dom... -

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Basic information

Entry
Database: PDB / ID: 2lup
TitleRDC refined solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (rnt1p) in complex with the terminal RNA hairpin of snr47 precursor
Components
  • RNA (32-MER)
  • Ribonuclease 3
KeywordsRNA BINDING PROTEIN/RNA / DSRBD / RNT1P / SNR47 / double strand RNA binding / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription ...box C/D sno(s)RNA processing / box H/ACA sno(s)RNA processing / regulation of fungal-type cell wall organization / termination of RNA polymerase II transcription, exosome-dependent / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / U4 snRNA 3'-end processing / ribonuclease III / ribonuclease III activity / termination of RNA polymerase II transcription / rRNA transcription / rRNA processing / double-stranded RNA binding / chromatin organization / nucleolus / nucleoplasm / nucleus
Similarity search - Function
Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...Ribonuclease III, N-terminal domain / Rnt1/Pac1, double-stranded RNA binding domain, fungi / Ribonuclease III N-terminal domain / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Ribonuclease 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Z. / Feigon, J.
Citation
Journal: Structure / Year: 2011
Title: Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs.
Authors: Wang, Z. / Hartman, E. / Roy, K. / Chanfreau, G. / Feigon, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III.
Authors: Wu, H. / Henras, A. / Chanfreau, G. / Feigon, J.
History
DepositionJun 19, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (32-MER)
B: Ribonuclease 3


Theoretical massNumber of molelcules
Total (without water)20,1282
Polymers20,1282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (32-MER)


Mass: 10305.164 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Ribonuclease 3 / Ribonuclease III / RNase III


Mass: 9822.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RNT1, YM9408.01C, YM9959.21, YMR239C / Variant: YMR239C / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q02555

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HBHA(CO)NH
1413D HNCO
1523D (H)CCH-TOCSY
1623D (H)CCH-COSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
90 %H2O-21
10 %D2O-3[U-100% 2H]1
20 mMsodium phosphate-41
150 mMsodium chloride-51
1 mMentity_1-6[U-100% 13C; U-100% 15N]2
90 %D2O-7[U-100% 2H]2
10 %sodium chloride-82
150 mMsodium phosphate-92
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THIS STRUCTURE IS AN RDC REFINED STRUCTURE OF PDB ENTRY 1T4L USING THE SAME RESTRAINTS PLUS ADDITIONAL RDCS [81 RDCS (REFINED) VS 43 RDCS (1T4L)].
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 16

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