[English] 日本語
Yorodumi
- PDB-5j2w: Intermediate state lying on the pathway of release of Tat from HI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j2w
TitleIntermediate state lying on the pathway of release of Tat from HIV-1 TAR.
Components
  • Apical region (29mer) of the HIV-1 TAR RNA element
  • Cyclic peptide mimetic of HIV-1 Tat
KeywordsVIRAL PROTEIN / TAR:Tat complex / RAM simulations / Residual dipolar couplings / intermediate excited state
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / molecular dynamics
AuthorsBorkar, A.N. / Bardaro Jr., M.F. / Varani, G. / Vendruscolo, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of a low-population binding intermediate in protein-RNA recognition.
Authors: Borkar, A.N. / Bardaro, M.F. / Camilloni, C. / Aprile, F.A. / Varani, G. / Vendruscolo, M.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 23, 2019Group: Data collection / Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units
Revision 1.5Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic peptide mimetic of HIV-1 Tat
B: Apical region (29mer) of the HIV-1 TAR RNA element


Theoretical massNumber of molelcules
Total (without water)11,0762
Polymers11,0762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1430 Å2
ΔGint2 kcal/mol
Surface area6210 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3871structures with the lowest energy
RepresentativeModel #1target function

-
Components

#1: Protein/peptide Cyclic peptide mimetic of HIV-1 Tat


Mass: 1768.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#2: RNA chain Apical region (29mer) of the HIV-1 TAR RNA element


Mass: 9307.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: Not applicable

-
Sample preparation

DetailsType: solution
Contents: 2 uM [U-99% 13C; U-99% 15N] TAR and Tatp, 100% D2O
Label: TAR:Tatp / Solvent system: 100% D2O
SampleConc.: 2 uM / Component: TAR and Tatp / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 298.15 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

-
Processing

NMR softwareName: Gromacs, Plumed / Developer: Vendruscolo, Camilloni, Borkar and others / Classification: structure calculation
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Replica averaged metadynamics (RAM) simulations
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3871 / Conformers submitted total number: 10

+
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