[English] 日本語
Yorodumi
- PDB-2m39: The solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m39
TitleThe solution structure of 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX
ComponentsRNA (5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3')
KeywordsRNA / DUPLEX / (3' / 5')-RNA / 2'-O-(2-METHOXYETHYL) RIBOSE
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesSynthetic (others)
MethodSOLUTION NMR / simulated annealing, energy minimization
Model detailslowest energy, model7
AuthorsPlevnik, M. / Cevec, M. / Plavec, J.
CitationJournal: Biochimie / Year: 2013
Title: NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex.
Authors: Plevnik, M. / Cevec, M. / Plavec, J.
History
DepositionJan 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
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(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3')
B: RNA (5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3')


Theoretical massNumber of molelcules
Total (without water)9,0692
Polymers9,0692
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)9 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA (5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L)P*DG)-3')


Mass: 4534.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE CHEMISTRY / Source: (synth.) Synthetic (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D NOESY
1222D NOESY
1322D DQF-COSY
NMR detailsText: STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- AND HETERONUCLEAR TECHNIQUES.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
22.5 mM 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3', 100 mM potassium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2.5 mM5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-11
100 mMpotassium chloride-21
2.5 mM5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3'-32
100 mMpotassium chloride-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007ambient 303 K
21007ambient 278 K

-
NMR measurement

NMR spectrometerType: Varian Unity Inova / Manufacturer: Varian / Model: Unity Inova / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
VNMR6.1BVarianprocessing
Felix2000Accelrys Software Inc.processing
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmanstructure solution
Amber7Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, Kollmanrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY ...Details: STRUCTURES WERE REFINED BY NMR RESTRAINED MOLECULAR DYNAMICS IN TWO STAGES USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL. THE RESULTING STRUCTURES WERE SUBJECTED TO ENERGY MINIMIZATION. 3',5'-PHOSPHODIESTER LINKAGES BETWEEN RESIDUES, O2' OF EACH RIBOSE MODIFIED BY METHOXYETHYL.
NMR constraintsNOE constraints total: 394
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 9

+
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