[English] 日本語
Yorodumi
- PDB-1tbc: HIV-1 TAT, NMR, 10 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tbc
TitleHIV-1 TAT, NMR, 10 STRUCTURES
ComponentsTAT PROTEIN
KeywordsTRANSCRIPTION REGULATION / HIV-1 / TRANSACTIVATION / RNA BINDING
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / regulatory region RNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation ...viral gene expression / trans-activation response element binding / regulatory region RNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / 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 / virus-mediated perturbation of host defense response / 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
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsRoesch, P. / Boehm, M. / Sticht, H.
Citation
Journal: To be Published
Title: Solution Structure of HIV-1 Tat Protein
Authors: Boehm, M. / Sticht, H. / Seidel, G. / Roesch, P.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Structural Studies of HIV-1 Tat Protein
Authors: Bayer, P. / Kraft, M. / Ejchart, A. / Westendorp, M. / Frank, R. / Rosch, P.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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: TAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,7391
Polymers9,7391
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 / 240ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Representative

-
Components

#1: Protein TAT PROTEIN / TRANSACTIVATING REGULATORY PROTEIN


Mass: 9739.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: BL21 / Gene: TATCYS- / Variant: ZAIRE 2 / Plasmid: BL21 / Species (production host): Escherichia coli / Gene (production host): TATCYS- / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12506

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
1411H-15N-HSQC
1511H
1611H
17115N-NOESY-HMQC
1811H
1911H
110115N-TOCSY-HMQC

-
Sample preparation

DetailsContents: H2O/D2O (9:1)
Sample conditionsIonic strength: 0.85 M / pH: 5.0 / Pressure: 10E+5 PA atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
NDEEstructure solution
SYBYLstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 240 / 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