[English] 日本語
Yorodumi
- PDB-1mv1: The Tandem, Sheared PA Pairs in 5'(rGGCPAGCCU)2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mv1
TitleThe Tandem, Sheared PA Pairs in 5'(rGGCPAGCCU)2
Components5'-R(*GP*GP*CP*(P5P)P*AP*GP*CP*CP*U)-3'
KeywordsRNA / ribonucleic acid / duplex / tandem mismatch / purine
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsZnosko, B.M. / Burkard, M.E. / Krugh, T.R. / Turner, D.H.
Citation
Journal: Biochemistry / Year: 2002
Title: Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2
Authors: Znosko, B.M. / Burkard, M.E. / Krugh, T.R. / Turner, D.H.
#1: Journal: Biochemistry / Year: 2002
Title: Sheared Aanti-Aanti Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2
Authors: Znosko, B.M. / Burkard, M.E. / Schroeder, S.J. / Krugh, T.R. / Turner, D.H.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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
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: 5'-R(*GP*GP*CP*(P5P)P*AP*GP*CP*CP*U)-3'
B: 5'-R(*GP*GP*CP*(P5P)P*AP*GP*CP*CP*U)-3'


Theoretical massNumber of molelcules
Total (without water)5,7122
Polymers5,7122
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)1 / -
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain 5'-R(*GP*GP*CP*(P5P)P*AP*GP*CP*CP*U)-3'


Mass: 2855.769 Da / Num. of mol.: 2 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
22mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 99.996% D2O99.996% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
190% H2O, 10% D2O 6.5ambient 273 K
299.996% D2O 7.7ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Variancollection
Felix2000MSIdata analysis
Discover95MSIstructure solution
Discover95MSIrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: The structure is based on a total of 86 interproton distance restraints per strand, 18 hydrogen bond restraints, and 46 dihedral angle restraints per strand.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers submitted total number: 1

+
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