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- PDB-1t4l: Solution structure of double-stranded RNA binding domain of S. ce... -

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Basic information

Entry
Database: PDB / ID: 1t4l
TitleSolution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with the 5' terminal RNA hairpin of snR47 precursor
Components
  • 5' terminal hairpin of snR47 precursor
  • Ribonuclease III
KeywordsRNA BINDING PROTEIN/RNA / dsRBD / RNase III / AGNN tetraloop / protein-RNA complex / 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
AuthorsWu, H. / Henras, A. / Chanfreau, G. / Feigon, J.
CitationJournal: 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 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: 5' terminal hairpin of snR47 precursor
B: Ribonuclease III


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)15 / 100structures with the lowest energy
Representative

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Components

#1: RNA chain 5' terminal hairpin of snR47 precursor


Mass: 10305.164 Da / Num. of mol.: 1 / Fragment: AGAA tetraloop RNA hairpin / Source method: obtained synthetically
#2: Protein Ribonuclease III / RNase III


Mass: 9822.364 Da / Num. of mol.: 1 / Fragment: double-stranded RNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / 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 NOESY
1222D TOCSY
1333D CBCA(CO)NH
1433D CBCANH
1533D HBHA(CO)NH
1633D 15N-NOESY-HSQC
1743D 13C-NOESY-HMQC
1852D 13C-filtered/edited NOESY
1963D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
115N-labeled Rnt1p dsRBD/unlabeled snR47h95% H2O/5% D2O
2unlabeled Rnt1p dsRBD/unlabeled snR47h99.999% D2O
3uniformally 13C,15N-labeled Rnt1p dsRBD/unlabeled snR47h95% H2O/5% D2O
4uniformally 13C,15N-labeled Rnt1p dsRBD/unlabeled snR47h99.999% D2O
5unlabeled Rnt1p dsRBD/13C,15N-A,U,G,C-slectively labeled snR47h snR47h99.999% D2O
6unlabeled Rnt1p dsRBD/uniformally 13C,15N-labeled snR47h snR47h99.999% D2O
Sample conditionsIonic strength: 20mM NaPi, 150 mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIHBrungerrefinement
Felix2000Moleular Simulation Inc.data analysis
XwinNMR2.6Brukercollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 2359 distance restraints 225 dihedral restraints 43 residual dipolar couplings
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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