[English] 日本語
Yorodumi
- PDB-2ldl: Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ldl
TitleSolution NMR Structure of the HIV-1 Exon Splicing Silencer 3
ComponentsRNA (27-MER)
KeywordsRNA / exon splicing silencer
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMishler, C. / Levengood, J.D. / Johnson, C.A. / Rajan, P. / Znosko, B.M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Solution Structure of the HIV-1 Exon Splicing Silencer 3.
Authors: Levengood, J.D. / Rollins, C. / Mishler, C.H. / Johnson, C.A. / Miner, G. / Rajan, P. / Znosko, B.M. / Tolbert, B.S.
History
DepositionMay 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,6501
Polymers8,6501
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)12 / 256structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA (27-MER)


Mass: 8650.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Human immunodeficiency virus 1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D HNN-COSY
1312D 1H-1H NOESY
1412D 1H-1H TOCSY
1512D 1H-13C HMQC

-
Sample preparation

DetailsContents: 1-2 mM RNA (27-MER), 0.5-1 mM [U-100% 15N] RNA (27-MER), 0.5-1 mM [U-100% 13C] RNA (27-MER), 0.5-1 mM [U-2H] RNA (27-MER), 120 mM potassium chloride, 20 mM potassium phosphate, 10 mM ...Contents: 1-2 mM RNA (27-MER), 0.5-1 mM [U-100% 15N] RNA (27-MER), 0.5-1 mM [U-100% 13C] RNA (27-MER), 0.5-1 mM [U-2H] RNA (27-MER), 120 mM potassium chloride, 20 mM potassium phosphate, 10 mM cacodylate, 0.5 mM EDTA, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (27-MER)-11-21
mMRNA (27-MER)-2[U-100% 15N]0.5-11
mMRNA (27-MER)-3[U-100% 13C]0.5-11
mMRNA (27-MER)-4[U-2H]0.5-11
120 mMpotassium chloride-51
20 mMpotassium phosphate-61
10 mMcacodylate-71
0.5 mMEDTA-81
Sample conditionsIonic strength: 150 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE6002
Bruker DMXBrukerDMX5003

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 362 / NOE intraresidue total count: 170 / NOE long range total count: 18 / NOE sequential total count: 174
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 12

+
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