[English] 日本語
Yorodumi
- PDB-1d0u: SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d0u
TitleSOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN
ComponentsPHAGE MS2 RNA BINDING SITE
KeywordsRNA / RNA HAIRPIN / BULGED BASE / STEM-LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics refinement
Model type detailsminimized average
AuthorsSmith, J.S. / Nikonowicz, E.P.
CitationJournal: Biochemistry / Year: 2000
Title: Phosphorothioate substitution can substantially alter RNA conformation.
Authors: Smith, J.S. / Nikonowicz, E.P.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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: PHAGE MS2 RNA BINDING SITE


Theoretical massNumber of molelcules
Total (without water)6,7291
Polymers6,7291
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)23 / 111back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1/2minimized average structure

-
Components

#1: RNA chain PHAGE MS2 RNA BINDING SITE


Mass: 6729.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Transcription by T7 RNA ploymerase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
2323D 13C-separated NOESY
2422D NOESY
252DQF-COSY
26231P-1H HETCOR
NMR detailsText: The structure was determined using standard 2D homonuclear and 2D/3D heteronuclear techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.2 mM replicase operator RNA U-15N,13C; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA90% H2O/10% D2O
22.2 mM replicase operator RNA U-15N,13C; 10 mM KPi buffer; 10 mM NaCl; 0.2 mM EDTA100% D2O
Sample conditionsIonic strength: ~50 mM / pH: 6.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
UXNMR1994Spectraspincollection
Felix1997Biosym-MSIprocessing
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing, molecular dynamics refinement / Software ordinal: 1
Details: structures were calculated using 469 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 ...Details: structures were calculated using 469 conformationally restrictive NOE distance constraints (i.e., intra-residue sugar-sugar NOEs are not included), 20 H-bond base pair constraints, 30 backbone dihedral restraints, and dihedral restraints to restrict sugar pucker conformation.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 111 / Conformers submitted total number: 23

+
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://pdbjlvh1.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