[English] 日本語
Yorodumi
- PDB-1jo7: Solution Structure of Influenza A Virus Promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jo7
TitleSolution Structure of Influenza A Virus Promoter
ComponentsInfluenza A virus promoter RNA
KeywordsRNA / RNA panhandle / AAU AC mismatch / bending / internal loop / UUCG
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance geometry, Simulated annealing + Susceptibility anisotropy
AuthorsBae, S.-H. / Cheong, H.-K. / Lee, J.-H. / Cheong, C. / Kainosho, M. / Choi, B.-S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural features of an influenza virus promoter and their implications for viral RNA synthesis.
Authors: Bae, S.H. / Cheong, H.K. / Lee, J.H. / Cheong, C. / Kainosho, M. / Choi, B.S.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Influenza A virus promoter RNA


Theoretical massNumber of molelcules
Total (without water)9,9131
Polymers9,9131
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)32 / 200The submitted conformer models are the 32 structures with lowest energy and acceptable covalent geometry
RepresentativeModel #1major conformers(1-15)

-
Components

#1: RNA chain Influenza A virus promoter RNA


Mass: 9912.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 in vitro transcription

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: DQF-COSY
NMR detailsText: The structure was determined using standard 2D and 3D techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM unlabeled90%H2O/10%D2O or 99.996% D2O
20.4mM 13C/15N labeled90%H2O/10%D2O or 99.996% D2O
30.4mM 13C/15N labeled90%H2O/10%D2O + PM (purple membrane)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM sodium phosphate 6.5ambient 294 K
210mM sodium phosphate 6.5ambient 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX4003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR98Bruker Inc.processing
Sparky3.95UCSFdata analysis
X-PLOR3.1Brunger et al.refinement
CNS1Brunger et al.refinement
RefinementMethod: Distance geometry, Simulated annealing + Susceptibility anisotropy
Software ordinal: 1
Details: The structures are refined using residual dipolar coupling constraints
NMR representativeSelection criteria: major conformers(1-15)
NMR ensembleConformer selection criteria: The submitted conformer models are the 32 structures with lowest energy and acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 32

+
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