[English] 日本語
Yorodumi
- PDB-1mfk: Structure of Prokaryotic SECIS mRNA Hairpin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mfk
TitleStructure of Prokaryotic SECIS mRNA Hairpin
Components5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*AP*CP*CP*GP*CP*C)-3'
KeywordsRNA / RNA tetraloop / (A/U)GNN tetraloop family / SelB
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsFourmy, D. / Guittet, E. / Yoshizawa, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of Prokaryotic SECIS mRNA Hairpin and its Interaction with Elongation Factor SELB
Authors: Fourmy, D. / Guittet, E. / Yoshizawa, S.
History
DepositionAug 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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
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: 5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*AP*CP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3861
Polymers7,3861
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)20 / 200structures with the lowest energy
Representative

-
Components

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


Mass: 7386.423 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SEQUENCE is from ESCHERICHIA COLI. T7 RNA polymerase in vitro transcription.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM SECIS RNA non-label; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
21mM SECIS RNA non-label; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
31mM SECIS RNA U-15N, 13C; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
41mM SECIS RNA U-15N, 13C; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
51mM SECIS RNA U-15N; 2mM phosphate buffer, pH 6.4; 100% D2O100% D2O
61mM SECIS RNA U-15N; 2mM phosphate buffer, pH 6.4; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.4ambient 275 K
26.4ambient 278 K
36.4ambient 288 K
46.4ambient 293 K
56.4ambient 303 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 DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameDeveloperClassification
DiscoverMOLECULAR SIMULATIONS INC.structure solution
DiscoverMOLECULAR SIMULATIONS INC.refinement
AURELIAdata analysis
XwinNMRprocessing
Gifaprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 260 NOE-derived distance constraints, 72 dihedral angle restraints
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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://pdbjlc1.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