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- PDB-2lbs: Solution structure of double-stranded RNA binding domain of S. ce... -

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Basic information

Entry
Database: PDB / ID: 2lbs
TitleSolution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with AAGU tetraloop hairpin
Components
  • RNA (32-MER)
  • Ribonuclease 3
KeywordsHYDROLASE/RNA / dsRBD / AAGU tetraloop / HYDROLASE-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 / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsWang, Z. / Hartman, E. / Roy, K. / Chanfreau, G. / 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
DepositionApr 6, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release

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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)20,1042
Polymers20,1042
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)16 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (32-MER)


Mass: 10282.124 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 / Fragment: DRBM domain residues 366-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNT1, YM9408.01C, YM9959.21, YMR239C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q02555, ribonuclease III

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-1H TOCSY
1342D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HN(CA)CB
1623D (H)CCH-TOCSY
1723D (H)CCH-COSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11032D 1H-1H COSY
11132D FILTERED/EDITED NOESY
11212D 1H-15N HSQC IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid, 90% H2O/10% D2O90% H2O/10% D2O
20.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid, 100% D2O100% D2O
30.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid, 100% D2O100% D2O
40.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein_1-1[U-100% 13C; U-100% 15N]0.8-11
mMprotein_2-21-21
mMprotein_1-3[U-100% 13C; U-100% 15N]0.8-12
mMprotein_2-41-22
mMprotein_1-50.8-13
mMprotein_2-6[U-100% 13C; U-100% 15N]1-23
mMprotein_1-70.8-14
mMprotein_2-8[U-100% 13C; U-100% 15N]1-24
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR_NIH2.24Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRView5.2.2Johnson, One Moon Scientificchemical shift assignment
NMRView5.2.2Johnson, One Moon Scientificdata analysis
NMRView5.2.2Johnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
TOPSPIN2Bruker Biospincollection
xwinnmrBruker Biospincollection
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 3600 / NOE intraresidue total count: 1085 / NOE long range total count: 467 / NOE medium range total count: 415 / NOE sequential total count: 823
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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