[English] 日本語
Yorodumi
- EMDB-3335: Cryo electron microscopy of a complex of Tor-1190RFP and Lst8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3335
TitleCryo electron microscopy of a complex of Tor-1190RFP and Lst8
Map dataReconstruction of a complex of variant Tor-1190RFP and Lst8.
Sample
  • Sample: Complex of Tor-1190RFP with Lst8
  • Protein or peptide: Target of rapamycin (Tor)
  • Protein or peptide: Lst8
  • Protein or peptide: Red fluorescent protein (RFP)
Keywordscryo-EM / Tor / Lst8 / mTOR / kinase / PIKK / S/T protein kinase / TORC1 / mTORC1 / RFP
Function / homologyTORC1 complex / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Red fluorescent protein drFP583
Function and homology information
Biological speciesKluyveromyces marxianus (yeast) / Discosoma sp. (sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsBaretic D / Berndt A / Ohashi Y / Johnson CM / Williams RL
CitationJournal: Nat Commun / Year: 2016
Title: Tor forms a dimer through an N-terminal helical solenoid with a complex topology.
Authors: Domagoj Baretić / Alex Berndt / Yohei Ohashi / Christopher M Johnson / Roger L Williams /
Abstract: The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 ...The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 heterodimer forms a common sub-complex. We have determined the cryo-electron microscopy (EM) structure of Tor bound to Lst8. Two Tor-Lst8 heterodimers assemble further into a dyad-symmetry dimer mediated by Tor-Tor interactions. The first 1,300 residues of Tor form a HEAT repeat-containing α-solenoid with four distinct segments: a highly curved 800-residue N-terminal 'spiral', followed by a 400-residue low-curvature 'bridge' and an extended 'railing' running along the bridge leading to the 'cap' that links to FAT region. This complex topology was verified by domain insertions and offers a new interpretation of the mTORC1 structure. The spiral of one TOR interacts with the bridge of another, which together form a joint platform for the Regulatory Associated Protein of TOR (RAPTOR) regulatory subunit.
History
DepositionFeb 16, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseApr 13, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3335.png

Downloads & links

-
Map

FileDownload / File: emd_3335.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a complex of variant Tor-1190RFP and Lst8.
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.14
Minimum - Maximum-0.25997022 - 0.39881754
Average (Standard dev.)0.00099638 (±0.02979161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 428.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z428.800428.800428.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2600.3990.001

-
Supplemental data

-
Sample components

-
Entire : Complex of Tor-1190RFP with Lst8

EntireName: Complex of Tor-1190RFP with Lst8
Components
  • Sample: Complex of Tor-1190RFP with Lst8
  • Protein or peptide: Target of rapamycin (Tor)
  • Protein or peptide: Lst8
  • Protein or peptide: Red fluorescent protein (RFP)

-
Supramolecule #1000: Complex of Tor-1190RFP with Lst8

SupramoleculeName: Complex of Tor-1190RFP with Lst8 / type: sample / ID: 1000 / Oligomeric state: Dimer of Tor-1190RFP/Lst8 heterodimers / Number unique components: 3
Molecular weightTheoretical: 738 KDa

-
Macromolecule #1: Target of rapamycin (Tor)

MacromoleculeName: Target of rapamycin (Tor) / type: protein_or_peptide / ID: 1 / Name.synonym: Tor / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 277 KDa
Recombinant expressionOrganism: Kluyveromyces marxianus (yeast)
SequenceGO: TORC1 complex

-
Macromolecule #2: Lst8

MacromoleculeName: Lst8 / type: protein_or_peptide / ID: 2 / Name.synonym: Lethal with SEC13 protein 8 / Number of copies: 2 / Recombinant expression: Yes
Source (natural)Organism: Kluyveromyces marxianus (yeast)
Molecular weightTheoretical: 34 KDa
Recombinant expressionOrganism: Kluyveromyces marxianus (yeast)

-
Macromolecule #3: Red fluorescent protein (RFP)

MacromoleculeName: Red fluorescent protein (RFP) / type: protein_or_peptide / ID: 3 / Name.synonym: RFP, dsRed, FP583
Details: The tandem RFP was inserted between residues M1190 and D1191 of K. marxianus Target of rapamycin (Tor) polypeptide chain.
Number of copies: 4 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Discosoma sp. (sea anemone) / synonym: Coral anemones
Molecular weightTheoretical: 54 KDa
Recombinant expressionOrganism: Kluyveromyces marxianus (yeast)
SequenceUniProtKB: Red fluorescent protein drFP583

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4
Details: 50 mM Hepes pH 7.4 (23 deg C), 75 mM KCl, 250 mM NaCl, 0.3 % (v/v) CHAPS, 1 mM TCEP
GridDetails: Quantifoil Au R 1.2/1.3, 300 mesh grids, blotted for 11-13 s at 4 deg C
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: 11-13 s at 4 deg C

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105263 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateDec 12, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 518 / Average electron dose: 40 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle (Gctf)
Final angle assignmentDetails: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: OTHER / Software - Name: RELION
Details: Final map was calculated after masked classification with density subtraction on a single RFP tag.
Number images used: 5191
DetailsProcessed with RELION. CTF corrected each particle.
FSC plot (resolution estimation)

+
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