[English] 日本語
Yorodumi
- PDB-1t4l: Solution structure of double-stranded RNA binding domain of S. ce... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more