[English] 日本語
Yorodumi
- PDB-2kit: The solution structure of the reduced yeast TOR1 FATC domain boun... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kit
TitleThe solution structure of the reduced yeast TOR1 FATC domain bound to DPC micelles at 298K
ComponentsSerine/threonine-protein kinase TOR1
KeywordsTRANSFERASE / protein / dpc micelle / membrane-mimetic / ATP-binding / Cell cycle / Cell membrane / Kinase / Membrane / Nucleotide-binding / Serine/threonine-protein kinase / Vacuole
Function / homology
Function and homology information


TOR complex / regulation of snRNA pseudouridine synthesis / regulation of sphingolipid biosynthetic process / mitochondria-nucleus signaling pathway / fungal-type cell wall organization / TORC1 complex / TORC1 signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / negative regulation of macroautophagy ...TOR complex / regulation of snRNA pseudouridine synthesis / regulation of sphingolipid biosynthetic process / mitochondria-nucleus signaling pathway / fungal-type cell wall organization / TORC1 complex / TORC1 signaling / fungal-type vacuole membrane / cellular response to nitrogen starvation / negative regulation of macroautophagy / nucleolar large rRNA transcription by RNA polymerase I / TOR signaling / response to nutrient / negative regulation of autophagy / response to endoplasmic reticulum stress / meiotic cell cycle / regulation of cell growth / translational initiation / ribosome biogenesis / cellular response to heat / cellular response to oxidative stress / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / regulation of cell cycle / endosome membrane / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / protein-containing complex binding / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / : ...Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TOR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsDames, S.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Basis for the Association of the Redox-sensitive Target of Rapamycin FATC Domain with Membrane-mimetic Micelles.
Authors: Dames, S.A.
History
DepositionMay 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
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: Serine/threonine-protein kinase TOR1


Theoretical massNumber of molelcules
Total (without water)3,9631
Polymers3,9631
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Serine/threonine-protein kinase TOR1 / Phosphatidylinositol kinase homolog TOR1 / Target of rapamycin kinase 1 / Dominant rapamycin ...Phosphatidylinositol kinase homolog TOR1 / Target of rapamycin kinase 1 / Dominant rapamycin resistance protein 1


Mass: 3963.473 Da / Num. of mol.: 1 / Fragment: yeast TOR1 FATC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DRR1, J1803, TOR1, YJR066W / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta (DE3)
References: UniProt: P35169, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: The solution struture of the reduced yeast TOR1 FATC domain bound to DPC micelles at 298K
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D HNCA
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D HACAHB-COSY
11013D HNHB
1111{15N} SED 1H-13C HSQC
1121{13C'} SED 1H-13C HSQC
113115N T1
114115N T2
1151{1H}-15N-NOE

-
Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] y1fatc-1, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.5 mM / Component: y1fatc-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
NMRView5.2.2_01Johnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurstructure analysis
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
XwinNMR3.5Bruker Biospinprocessing
TENSOR22P. Dosset, D. Marion, M. Blackledgeanalysis of 15n relaxation data
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1167
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.5 Å

+
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