[English] 日本語
Yorodumi
- PDB-1k5k: Homonuclear 1H Nuclear Magnetic Resonance Assignment and Structur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k5k
TitleHomonuclear 1H Nuclear Magnetic Resonance Assignment and Structural Characterization of HIV-1 Tat Mal Protein
ComponentsTAT protein
KeywordsTRANSCRIPTION / HIV-1 / TAT / REGULATORY PROTEIN / AFRICAN VARIANT / NMR.
Function / homology
Function and homology information


: / trans-activation response element binding / positive regulation of viral transcription / modulation by virus of host chromatin organization / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation / RNA-binding transcription regulator activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II ...: / trans-activation response element binding / positive regulation of viral transcription / modulation by virus of host chromatin organization / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation / RNA-binding transcription regulator activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / DNA-templated transcription / extracellular region / metal ion binding
Similarity search - Function
HIV-1 Transactivator Protein / Tat domain / Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / Few Secondary Structures / Irregular
Similarity search - Domain/homology
MethodSOLUTION NMR / molecular dynamics
AuthorsGregoire, C. / Peloponese, J.M. / Esquieu, D. / Opi, S. / Campbell, G. / Solomiac, M. / Lebrun, E. / Lebreton, J. / Loret, E.P.
CitationJournal: Biopolymers / Year: 2001
Title: Homonuclear (1)H-NMR assignment and structural characterization of human immunodeficiency virus type 1 Tat Mal protein.
Authors: Gregoire, C. / Peloponese Jr., J.M. / Esquieu, D. / Opi, S. / Campbell, G. / Solomiac, M. / Lebrun, E. / Lebreton, J. / Loret, E.P.
History
DepositionOct 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Remark 999SEQUENCE THIS IS A SYNTHETIC PROTEIN WHICH HAS THE FULL BIOLOGICAL ACTIVITIES OF NATURAL TAT. ...SEQUENCE THIS IS A SYNTHETIC PROTEIN WHICH HAS THE FULL BIOLOGICAL ACTIVITIES OF NATURAL TAT. PELOPONESE ET AL. (1999) J. BIOL. CHEM. 274, 11473-11479.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TAT protein


Theoretical massNumber of molelcules
Total (without water)10,0561
Polymers10,0561
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)10 / 20back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

-
Components

#1: Protein TAT protein / Transactivating regulatory protein


Mass: 10056.459 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN HUMAN IMMUNODEFICIENCY VIRUS-1.
References: UniProt: P04613

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using four NMR experiments (TOCSY, NOESY 100 ms, NOESY 150 ms & NOESY 200 ms).

-
Sample preparation

DetailsContents: 1 mM Tat Mal; 100mM phosphate buffer; 90% H20 10% D2O; Azide 2/1000
Sample conditionspH: 4.5 / Pressure: Ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Felix972MSIdata analysis
Discover2000MSIstructure solution
Discover2000MSIrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 20 / 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://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