[English] 日本語
Yorodumi
- PDB-1akx: HIV-2 TRANS ACTIVATING REGION RNA COMPLEX WITH ARGININAMIDE, NMR,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1akx
TitleHIV-2 TRANS ACTIVATING REGION RNA COMPLEX WITH ARGININAMIDE, NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsTAR RNA
KeywordsRNA / TRANSCRIPTIONAL ACTIVATION / COMPLEX (RNA-LIGAND) / PROTEIN-RNA INTERACTIONS
Function / homologyARGININE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / RANDOM COORDINATES, SIMULATED ANNEALING
AuthorsBrodsky, A.S. / Williamson, J.R.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of the HIV-2 TAR-argininamide complex.
Authors: Brodsky, A.S. / Williamson, J.R.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents
Authors: Gelbin, A. / Schneider, B. / Clowny, L. / Hsieh, S.-H. / Olsen, W.K. / Berman, H.M.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: The Structure of the Human Immunodeficiency Virus Type-1 Tar RNA Reveals Principles of RNA Recognition by Tat Protein
Authors: Aboul-Ela, F. / Karn, J. / Varani, G.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Role of RNA Structure in Arginine Recognition of Tar RNA
Authors: Puglisi, J.D. / Chen, L. / Frankel, A.D. / Williamson, J.R.
#4: Journal: Science / Year: 1992
Title: Conformation of the Tar RNA-Arginine Complex by NMR Spectroscopy
Authors: Puglisi, J.D. / Tan, R. / Calnan, B.J. / Frankel, A.D. / Williamson, J.R.
History
DepositionMay 27, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: TAR RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8282
Polymers9,6531
Non-polymers1751
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20LEAST RESTRAINTS AND LOWEST ENERGY
Representative

-
Components

#1: RNA chain TAR RNA / TAR


Mass: 9652.761 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE PAPER

-
Sample preparation

Sample conditionspH: 6.4 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXR500VarianVXR5005001
Varian UNITYPLUSVarianUNITYPLUS5912
HOME MADE HOME MADEHOME MADEHOME MADE7503

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: RANDOM COORDINATES, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINTS AND LOWEST ENERGY
Conformers calculated total number: 20 / Conformers submitted total number: 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