[English] 日本語
Yorodumi
- PDB-2lv0: Solution Structure of Helix-35 Stem-loop from E. coli 23S rRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lv0
TitleSolution Structure of Helix-35 Stem-loop from E. coli 23S rRNA
ComponentsRNA (5'-R(*GP*GP*GP*CP*UP*AP*AP*UP*GP*UP*UP*GP*AP*AP*AP*AP*AP*UP*UP*AP*GP*CP*CP*C)-3')
KeywordsRNA / ribosome / 23S rRNA / methylation / erythromycin resistance
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsNikonowicz, E.P. / Wang, J. / Moran, S. / Donarski, J.
CitationJournal: To be Published
Title: Solution Structure of Helix-35 Stem-loop from E. coli 23S rRNA
Authors: Moran, S. / Donarski, J. / Wang, J. / Nikonowicz, E.P.
History
DepositionJun 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*GP*CP*UP*AP*AP*UP*GP*UP*UP*GP*AP*AP*AP*AP*AP*UP*UP*AP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7181
Polymers7,7181
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)11 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA (5'-R(*GP*GP*GP*CP*UP*AP*AP*UP*GP*UP*UP*GP*AP*AP*AP*AP*AP*UP*UP*AP*GP*CP*CP*C)-3')


Mass: 7717.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2142D 1H-15N HSQC
1212D 1H-13C HSQC
1313D (H)CCH-TOCSY
1413D 1H-13C NOESY
1522D 1H-1H NOESY
1622D DQF-COSY
2732D 1H-1H NOESY
1813D (H)CCH-COSY
1922D 1H-31P HETCOR
11012D 1H-15N HMQC
11112D 1H-13C ctHSQC-31P
11212D 1H-15N HCN
21343D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-99% 13C; U-99% 15N] RNA, 10 mM potassium phosphate, 10 mM sodium chloride, 0.1 mM EDTA, 100% D2O100% D2O
21.6 mM RNA, 10 mM potassium phosphate, 10 mM sodium chloride, 0.1 mM EDTA, 100% D2O100% D2O
31.6 mM RNA, 10 mM potassium phosphate, 10 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
41.2 mM [U-99% 13C; U-99% 15N] RNA, 10 mM potassium phosphate, 10 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMRNA-1[U-99% 13C; U-99% 15N]1
10 mMpotassium phosphate-21
10 mMsodium chloride-31
0.1 mMEDTA-41
1.6 mMRNA-52
10 mMpotassium phosphate-62
10 mMsodium chloride-72
0.1 mMEDTA-82
1.6 mMRNA-93
10 mMpotassium phosphate-103
10 mMsodium chloride-113
0.1 mMEDTA-123
1.2 mMRNA-13[U-99% 13C; U-99% 15N]4
10 mMpotassium phosphate-144
10 mMsodium chloride-154
0.1 mMEDTA-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.8ambient 298 K
2206.8ambient 283 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.refinement
VNMRVariancollection
VNMRVarianrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNA sugar pucker constraints total count: 22 / NOE constraints total: 345
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 11

+
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