[English] 日本語
Yorodumi
- PDB-6by5: Two-State 14-mer UUCG Tetraloop calculated from Exact NOEs (State... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6by5
TitleTwo-State 14-mer UUCG Tetraloop calculated from Exact NOEs (State one: Conformers 1-5, State Two: Conformers 6-10)
ComponentsRNA (5'-R(P*GP*GP*CP*AP*CP*UP*UP*CP*GP*GP*UP*GP*CP*C)-3')
KeywordsRNA / Exact NOE / UUCG tetraloop / 14-mer hairpin / Two-State
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNichols, P.J. / Henen, M.A. / Born, A. / Strotz, D. / Guntert, P. / Vogeli, B.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Colorado Anschutz Medical Campus United States
CitationJournal: Commun Biol / Year: 2018
Title: High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints.
Authors: Nichols, P.J. / Henen, M.A. / Born, A. / Strotz, D. / Guntert, P. / Vogeli, B.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / pdbx_nmr_representative
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_representative.conformer_id
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4551
Polymers4,4551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2990 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

-
Components

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


Mass: 4454.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D WATERGATE [1H-1H] NOESY buildup series
122isotropic12D PreSat [1H-1H] NOESY buildup series

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM KHPO4, 0.4 mM EDTA, 1 mM 14-mer UUCG Tetraloop, 95% H2O/5% D2OH2O Sample95% H2O/5% D2O
solution220 mM KHPO4, 0.4 mM EDTA, 1.7 mM 14-mer UUCG Tetraloop, 100% D2OD2O Sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMKHPO4natural abundance1
0.4 mMEDTAnatural abundance1
1 mM14-mer UUCG Tetraloopnatural abundance1
20 mMKHPO4natural abundance2
0.4 mMEDTAnatural abundance2
1.7 mM14-mer UUCG Tetraloopnatural abundance2
Sample conditionsIonic strength: 20 mM / Label: Conditions 1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian Varian Direct Drive / Manufacturer: Varian / Model: Varian Direct Drive / Field strength: 900 MHz
Details: 5 mm triple resonance 1H/13C/15N cold probe with z-axis gradient

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 4 / Details: Multi-State Calculation
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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