[English] 日本語
Yorodumi
- PDB-2l9e: Solution Structure of the human Anti-codon Stem and loop(hASL) of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l9e
TitleSolution Structure of the human Anti-codon Stem and loop(hASL) of transfer RNA Lysine 3 (tRNALys3)
ComponentsRNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average, model 1
Model type detailsminimized average
AuthorsVendeix, F.A.P. / Murphy IV, F.V. / Cantara, W. / Leszczynska, G. / Gustilo, E.M. / Sproat, B. / Malkiewicz, A.A.P. / Agris, P.F.
CitationJournal: To be Published
Title: Solution Structure of the human Anti-codon Stem and loop(hASL) of transfer RNA Lysine 3 (tRNALys3)
Authors: Vendeix, F.A.P. / Murphy IV, F.V. / Cantara, W. / Leszczynska, G. / Gustilo, E.M. / Sproat, B. / Malkiewicz, A.A.P. / Agris, P.F.
History
DepositionFeb 8, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,6451
Polymers5,6451
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 / 80structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: RNA chain RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')


Mass: 5644.539 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H TOCSY
2322D 1H-1H COSY
2422D DQF-COSY
2522D 1H-1H NOESY
2622D 1H-1H TOCSY
2722D 1H-13C HSQC
2822D 1H-31P HETCOR
2912D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.50 mM RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3'), 90% H2O/10% D2O90% H2O/10% D2O
21.50 mM RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3'), 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.50 mMRNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')-11
1.50 mMRNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*UP*CP*UP*GP*C)-3')-22
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1unknown 6.2ambient 275 K
2unknown 6.2ambient 295 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian UnityVarianUNITY6002

-
Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / 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