[English] 日本語
Yorodumi
- PDB-2kpv: NMR model of the first let-7 miRNA complementary site (LCS1) in 3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kpv
TitleNMR model of the first let-7 miRNA complementary site (LCS1) in 3'-UTR of lin-41 mRNA from C. elegans
ComponentsRNA (34-MER)
KeywordsRNA / stem-loop / adenine bulge / asymmetric internal loop / residual dipolar couplings / GAAA tetraloop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
Model detailsclosest to the average, model 1
AuthorsCevec, M. / Thibaudeau, C. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: NMR structure of the let-7 miRNA interacting with the site LCS1 of lin-41 mRNA from Caenorhabditis elegans.
Authors: Cevec, M. / Thibaudeau, C. / Plavec, J.
History
DepositionOct 20, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (34-MER)


Theoretical massNumber of molelcules
Total (without water)10,9551
Polymers10,9551
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)10 / 100structures with the lowest energy and least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA (34-MER)


Mass: 10954.567 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription using T7 RNA polymerase and DNA oligonucleotide template

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
2212D 15N-HSQC
1322D 13C-HSQC
1422D DQF-COSY
2512D HNN-COSY
1622D TOCSY
1722D 1H-31P COSY
1832D 15N-IPAP-HSQC
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11123D 13C-separated-NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM [U-100% 13C; U-100% 15N] RNA (34-MER)-1, 10mM sodium phosphate-2, 20mM sodium chloride-3, 95% H2O/5% D2O95% H2O/5% D2O
22mM [U-100% 13C; U-100% 15N] RNA (34-MER)-4, 10mM sodium phosphate-5, 20mM sodium chloride-6, 100% D2O100% D2O
31mM [U-100% 13C; U-100% 15N] RNA (34-MER)-7, 10mM sodium phosphate-8, 20mM sodium chloride-9, 17mg/mL Pf1 phage-10, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMRNA (34-MER)-1[U-100% 13C; U-100% 15N]1
10 mMsodium phosphate-21
20 mMsodium chloride-31
2 mMRNA (34-MER)-4[U-100% 13C; U-100% 15N]2
10 mMsodium phosphate-52
20 mMsodium chloride-62
1 mMRNA (34-MER)-7[U-100% 13C; U-100% 15N]3
10 mMsodium phosphate-83
20 mMsodium chloride-93
17 mg/mLPf1 phage-103
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.8ambient 303 K
2206.8ambient 278 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian NMR systemVarianNMR system8001
Varian NMR systemVarianNMR system6002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmrefinement
Felix2002Accelrys Software Inc.data analysis
Felix2002Accelrys Software Inc.processing
VnmrJ2.1BVariandata collection
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: 810 NOE-derived distance restraints, 138 torsion angle restraints, 52 residual dipolar coupling restraints, 32 hydrogen bond restraints and 24 planarity restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy and least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

+
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