[English] 日本語
Yorodumi
- PDB-1jfw: HOMONUCLEAR AND HETERONUCLEAR 1H-13C NUCLEAR MAGNETIC RESONANCE A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jfw
TitleHOMONUCLEAR AND HETERONUCLEAR 1H-13C NUCLEAR MAGNETIC RESONANCE ASSIGNMENT AND STRUCTURAL CHARACTERIZATION OF A HIV-1 TAT PROTEIN
ComponentsTAT PROTEIN
KeywordsVIRAL PROTEIN / TAT / HIV-1 / HETERONUCLEAR / DRUG DESIGN
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / regulatory region RNA binding / negative regulation of cellular respiration / positive regulation of viral transcription / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / membrane hyperpolarization ...viral gene expression / trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / regulatory region RNA binding / negative regulation of cellular respiration / positive regulation of viral transcription / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / membrane hyperpolarization / actinin binding / negative regulation of peptidyl-threonine phosphorylation / RNA-binding transcription regulator activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / positive regulation of protein localization to nucleus / positive regulation of NF-kappaB transcription factor activity / host cell cytoplasm / protein domain specific binding / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / SIMULATED ANNEALING, RANDOM LOOP RESEARCH VALIDATED WITH NOE BACK-CALCULATION ENERGY MINIMIZATION, MOLECULAR DYNAMIC
AuthorsPeloponese, J.M. / Gregoire, C. / Opi, S. / Esquieu, D.
CitationJournal: C.R.Acad.Sci.III / Year: 2000
Title: 1H-13C nuclear magnetic resonance assignment and structural characterization of HIV-1 Tat protein.
Authors: Peloponese Jr., J.M. / Gregoire, C. / Opi, S. / Esquieu, D. / Sturgis, J. / Lebrun, E. / Meurs, E. / Collette, Y. / Olive, D. / Aubertin, A.M. / Witvrow, M. / Pannecouque, C. / De Clercq, E. ...Authors: Peloponese Jr., J.M. / Gregoire, C. / Opi, S. / Esquieu, D. / Sturgis, J. / Lebrun, E. / Meurs, E. / Collette, Y. / Olive, D. / Aubertin, A.M. / Witvrow, M. / Pannecouque, C. / De Clercq, E. / Bailly, C. / Lebreton, J. / Loret, E.P.
History
DepositionJun 22, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionAug 15, 2001ID: 1FKU
Revision 1.0Aug 15, 2001Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,7891
Polymers9,7891
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)11 / 100BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Representative

-
Components

#1: Protein TAT PROTEIN / TRANSACTIVATING REGULATORY PROTEIN


Mass: 9789.319 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS SYNTHESIZED (SOLID PHASE SYNTHESIS). THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
References: UniProt: P04610

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1313D 13C-SEPARATED NOESY

-
Sample preparation

DetailsContents: SPECIFIC 13C LABELLING OF GLYCINE 15,44,48,61,79,83
Sample conditionspH: 4.50 / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DISCOVER 95, 97MSIrefinement
Felix95structure solution
97 AND98structure solution
NMR_REFINE97structure solution
HOMOLOGY95structure solution
97structure solution
98structure solution
RefinementMethod: SIMULATED ANNEALING, RANDOM LOOP RESEARCH VALIDATED WITH NOE BACK-CALCULATION ENERGY MINIMIZATION, MOLECULAR DYNAMIC
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 915 RESTRAINTS AND 272 ARE LONG-RANGE NOES.
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE ...Conformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMEN TAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Conformers calculated total number: 100 / Conformers submitted total number: 11

+
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