[English] 日本語
Yorodumi
- PDB-1exy: SOLUTION STRUCTURE OF HTLV-1 PEPTIDE BOUND TO ITS RNA APTAMER TARGET -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1exy
TitleSOLUTION STRUCTURE OF HTLV-1 PEPTIDE BOUND TO ITS RNA APTAMER TARGET
Components
  • HTLV-1 REX PEPTIDE
  • RNA APTAMER, 33-MER
KeywordsRNA BINDING PROTEIN/RNA / arginine-guanine sandwich / extended bound basic Rex peptide / flap base / junctional base triplets / RNA binding pocket architecture / RNA BINDING PROTEIN-RNA COMPLEX
Function / homologyhost cell nucleolus / mRNA transport / host cell cytoplasm / RNA binding / RNA / RNA (> 10) / Protein Rex / Protein Rex
Function and homology information
MethodSOLUTION NMR / simulated annealing with torsion angle dynamics
AuthorsJiang, F. / Gorin, A. / Hu, W. / Majumdar, A. / Baskerville, S. / Xu, W. / Ellington, A. / Patel, D.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Anchoring an extended HTLV-1 Rex peptide within an RNA major groove containing junctional base triples.
Authors: Jiang, F. / Gorin, A. / Hu, W. / Majumdar, A. / Baskerville, S. / Xu, W. / Ellington, A. / Patel, D.J.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMay 15, 2000ID: 1C4J
Revision 1.0May 15, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: RNA APTAMER, 33-MER
B: HTLV-1 REX PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,7702
Polymers12,7702
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)12 / 60structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: RNA chain RNA APTAMER, 33-MER


Mass: 10654.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: obtained by in vitro selection
#2: Protein/peptide HTLV-1 REX PEPTIDE / PROTEIN X (HTLV-1) / P27 PROTEIN (HTLV-1)


Mass: 2115.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide from HTLV-1 virus protein / References: UniProt: O56230, UniProt: P0C206*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121reviewed in the primary citation

-
Sample preparation

DetailsContents: 1.2-2.8 mM of the complex, 10mM sodium phosphate, 0.2 mM EDTA
Solvent system: H2O, D2O
Sample conditionsIonic strength: 10 mM / 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8Brunger, A.T.structure solution
X-PLOR3.8Brunger, A.T.refinement
RefinementMethod: simulated annealing with torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 12

+
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