[English] 日本語
Yorodumi
- PDB-1c0o: SOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c0o
TitleSOLUTION STRUCTURE OF THE P5 HAIRPIN FROM A GROUP I INTRON COMPLEXED WITH COBALT (III) HEXAMMINE, NMR, 19 CONVERGED STRUCTURES
ComponentsRNA (5'-R(*GP*GP*GP*UP*CP*UP*UP*CP*GP*GP*GP*UP*CP*C)-3')
KeywordsRNA / RIBONUCLEIC ACID / COBALT (III) HEXAMMINE / METAL BINDING / RNA STRUCTURE
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsColmenarejo, G. / Tinoco Jr., I.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme.
Authors: Colmenarejo, G. / Tinoco Jr., I.
History
DepositionMar 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,6332
Polymers4,4721
Non-polymers1611
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 40NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY
Representative

-
Components

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


Mass: 4471.667 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLOSED BY A UUCG TETRALOOP; COBALT (III) HEXAMMINE BINDS AT THE MAJOR GROOVE OF TWO TANDEM G-U WOBBLE PAIRS IN 5'-GU-3' ORIENTATION
Source: (gene. exp.) Tetrahymena thermophila (eukaryote)
Description: SYNTHESIZED ENZYMATICALLY IN-VITRO USING T7 RNA POLYMERASE
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121D2O NOESY
131H2O NOESY
141TOCSY
15113C-1H HMQC
16131P-1H HETCOR
17131P-1H TOCSY
18131P-1H TOCSY-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL 13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS LOCATED USING DOCKING WITH 7 ...Text: THE STRUCTURE WAS DETERMINED USING A NON-ISOTOPICALLY LABELLED RNA SAMPLE. ALL 13C EXPERIMENTS WERE DONE USING NATURAL ABUNDANCE. COBALT (III) HEXAMMINE WAS LOCATED USING DOCKING WITH 7 INTERMOLECULAR NOES OBSERVED IN 2D WATER NOESY EXPERIMENTS.

-
Sample preparation

DetailsContents: PHOSPHATE BUFFER, EDTA
Sample conditionsIonic strength: 100 mM NACL / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6005001
Bruker DRX500BrukerDRX5006002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
FELIX95structure solution
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NOE ENERGY (LEAST RESTRAINT VIOLATIONS), DIHEDRAL ENERGY (LEAST RESTRAINT VIOLATIONS), TOTAL ENERGY
Conformers calculated total number: 40 / Conformers submitted total number: 19

+
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