[English] 日本語
Yorodumi
- PDB-2ru7: Refined structure of RNA aptamer in complex with the partial bind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ru7
TitleRefined structure of RNA aptamer in complex with the partial binding peptide of prion protein
Components
  • P16 peptide from Major prion protein
  • RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
KeywordsMembrane Protein/RNA / Aptamer / Prion / RNA / Alzheimer's disease / Membrane protein-RNA complex
Function / homology
Function and homology information


type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta ...type 5 metabotropic glutamate receptor binding / cuprous ion binding / : / side of membrane / inclusion body / cellular response to copper ion / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / amyloid-beta binding / G-quadruplex RNA binding / microtubule binding / nuclear membrane / membrane raft / copper ion binding / dendrite / protein-containing complex binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
RNA / RNA (> 10) / Major prion protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / energy minimization, simulated annealing
Model detailslowest energy, model1
AuthorsHayashi, T. / Oshima, H. / Mashima, T. / Nagata, T. / Katahira, M. / Kinoshita, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.
Authors: Hayashi, T. / Oshima, H. / Mashima, T. / Nagata, T. / Katahira, M. / Kinoshita, M.
History
DepositionDec 24, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Category: citation / database_2 / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
B: RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')
C: P16 peptide from Major prion protein
D: P16 peptide from Major prion protein


Theoretical massNumber of molelcules
Total (without water)10,8424
Polymers10,8424
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')


Mass: 4033.512 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein/peptide P16 peptide from Major prion protein / PrP / Major scrapie-associated fibril protein 1


Mass: 1387.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Bos taurus (cattle) / References: UniProt: P10279

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2212D 1H-1H NOESY
1322D 1H-1H NOESY
2422D 1H-1H NOESY
2512D 1H-1H TOCSY
2622D 1H-1H TOCSY
2722D DQF-COSY
2822D 1H-13C HSQC
291JRHMBC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 mM P16-2, 10 mM potassium phosphate-3, 10 mM potassium chloride-4, 0.01 mM DSS-5, 3 mM sodium azide-6, 95% H2O/5% D2O95% H2O/5% D2O
21 mM RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 mM P16-8, 10 mM potassium phosphate-9, 10 mM potassium chloride-10, 0.01 mM DSS-11, 3 mM sodium azide-12, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-11
1 mMP16-21
10 mMpotassium phosphate-31
10 mMpotassium chloride-41
0.01 mMDSS-51
3 mMsodium azide-61
1 mMRNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-72
1 mMP16-82
10 mMpotassium phosphate-92
10 mMpotassium chloride-102
0.01 mMDSS-112
3 mMsodium azide-122
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 6.2 ambient atm278 K
210 6.2 ambient atm303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.26Schwieters, Kuszewski, Tjandra and Clorerefinement
Amber12Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: energy minimization, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 5 / Representative conformer: 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