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- PDB-1t4n: Solution structure of Rnt1p dsRBD -

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Basic information

Entry
Database: PDB / ID: 1t4n
TitleSolution structure of Rnt1p dsRBD
ComponentsRibonuclease III
KeywordsHYDROLASE / dsRBD / RNA-binding
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR
AuthorsLeulliot, N. / Quevillon-Cheruel, S. / Graille, M. / van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. ...Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. / Ares, M. / Varani, G.
CitationJournal: Embo J. / Year: 2004
Title: A new alpha-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III
Authors: Leulliot, N. / Quevillon-Cheruel, S. / Graille, M. / Van Tilbeurgh, H. / Leeper, T.C. / Godin, K.S. / Edwards, T.E. / Sigurdsson, S.T. / Rozenkrants, N. / Nagel, R.J. / Ares, M. / Varani, G.
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn ...database_2 / diffrn / diffrn_radiation / diffrn_radiation_wavelength / pdbx_nmr_software / 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_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)10,4531
Polymers10,4531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)51 / 51structures with acceptable covalent geometry
RepresentativeModel #1

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Components

#1: Protein Ribonuclease III / / RNase III / Rnt1p


Mass: 10453.133 Da / Num. of mol.: 1 / Fragment: dsRBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNT1, YMR239C, YM9408.01C, YM9959.21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02555, ribonuclease III

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 50mM NACL / pH: 6.5 / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCE DMXBrukerAVANCE DMX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
SparkyGoddardstructure calculation
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENstructure calculation
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 51 / Conformers submitted total number: 51

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