[English] 日本語
Yorodumi
- EMDB-12957: Cryo-EM structure of the human R2TP-TTT complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12957
TitleCryo-EM structure of the human R2TP-TTT complex
Map dataCryo-EM structure of the human R2TP-TTT complex
Sample
  • Complex: RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adaptor proteins
Function / homology
Function and homology information


: / positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / TORC2 complex / TORC1 complex ...: / positive regulation of DNA damage checkpoint / TTT Hsp90 cochaperone complex / promoter-enhancer loop anchoring activity / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / establishment of protein localization to chromatin / R2TP complex / TORC2 complex / TORC1 complex / dynein axonemal particle / Swr1 complex / RPAP3/R2TP/prefoldin-like complex / regulation of TOR signaling / regulation of double-strand break repair / positive regulation of telomerase RNA localization to Cajal body / Ino80 complex / protein folding chaperone complex / box C/D snoRNP assembly / regulation of chromosome organization / NuA4 histone acetyltransferase complex / telomeric DNA binding / regulation of DNA replication / TFIID-class transcription factor complex binding / regulation of embryonic development / MLL1 complex / Telomere Extension By Telomerase / positive regulation of double-strand break repair via homologous recombination / telomere maintenance via telomerase / RNA polymerase II core promoter sequence-specific DNA binding / regulation of DNA repair / Deposition of new CENPA-containing nucleosomes at the centromere / DNA helicase activity / positive regulation of DNA repair / TBP-class protein binding / telomere maintenance / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / Hsp90 protein binding / euchromatin / negative regulation of canonical Wnt signaling pathway / chromatin DNA binding / ADP binding / beta-catenin binding / nuclear matrix / transcription corepressor activity / UCH proteinases / cellular response to UV / nucleosome / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / protein folding / HATs acetylate histones / ATPase binding / spermatogenesis / regulation of apoptotic process / DNA recombination / DNA helicase / chromosome, telomeric region / molecular adaptor activity / transcription coactivator activity / nuclear body / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / chromatin remodeling / ribonucleoprotein complex / cadherin binding / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / DNA repair / centrosome / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Tti2 family / Tti2 family / TEL2-interacting protein 1 / : / TELO2-interacting protein 1 / Telomere length regulation protein, conserved domain / TEL2, C-terminal domain superfamily / Telomere length regulation protein / RuvB-like / RuvB-like, AAA-lid domain ...Tti2 family / Tti2 family / TEL2-interacting protein 1 / : / TELO2-interacting protein 1 / Telomere length regulation protein, conserved domain / TEL2, C-terminal domain superfamily / Telomere length regulation protein / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Armadillo-like helical / Armadillo-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TELO2-interacting protein 1 homolog / TELO2-interacting protein 2 / RuvB-like 2 / RuvB-like 1 / Telomere length regulation protein TEL2 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsPal M / Llorca O / Pearl L
Funding support United Kingdom, Spain, 4 items
OrganizationGrant numberCountry
Wellcome Trust095605/Z/11/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R01678X/1 United Kingdom
European Regional Development FundSAF2017-82632-P Spain
European Regional Development Fund Spain
CitationJournal: Cell Rep / Year: 2021
Title: Structure of the TELO2-TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone.
Authors: Mohinder Pal / Hugo Muñoz-Hernandez / Dennis Bjorklund / Lihong Zhou / Gianluca Degliesposti / J Mark Skehel / Emma L Hesketh / Rebecca F Thompson / Laurence H Pearl / Oscar Llorca / Chrisostomos Prodromou /
Abstract: The R2TP (RUVBL1-RUVBL2-RPAP3-PIH1D1) complex, in collaboration with heat shock protein 90 (HSP90), functions as a chaperone for the assembly and stability of protein complexes, including RNA ...The R2TP (RUVBL1-RUVBL2-RPAP3-PIH1D1) complex, in collaboration with heat shock protein 90 (HSP90), functions as a chaperone for the assembly and stability of protein complexes, including RNA polymerases, small nuclear ribonucleoprotein particles (snRNPs), and phosphatidylinositol 3-kinase (PI3K)-like kinases (PIKKs) such as TOR and SMG1. PIKK stabilization depends on an additional complex of TELO2, TTI1, and TTI2 (TTT), whose structure and function are poorly understood. The cryoelectron microscopy (cryo-EM) structure of the human R2TP-TTT complex, together with biochemical experiments, reveals the mechanism of TOR recruitment to the R2TP-TTT chaperone. The HEAT-repeat TTT complex binds the kinase domain of TOR, without blocking its activity, and delivers TOR to the R2TP chaperone. In addition, TTT regulates the R2TP chaperone by inhibiting RUVBL1-RUVBL2 ATPase activity and by modulating the conformation and interactions of the PIH1D1 and RPAP3 components of R2TP. Taken together, our results show how TTT couples the recruitment of TOR to R2TP with the regulation of this chaperone system.
History
DepositionMay 17, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0048
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0048
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12957.png

Downloads & links

-
Map

FileDownload / File: emd_12957.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the human R2TP-TTT complex
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.0048 / Movie #1: 0.0048
Minimum - Maximum-0.009024014 - 0.031790406
Average (Standard dev.)0.00042016292 (±0.0017494085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 293.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z293.440293.440293.440
α/β/γ90.00090.00090.000
start NX/NY/NZ29290
NX/NY/NZ140137200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0090.0320.000

-
Supplemental data

-
Half map: Cryo-EM structure of the human R2TP-TTT complex (half maps)

Fileemd_12957_half_map_1.map
AnnotationCryo-EM structure of the human R2TP-TTT complex (half maps)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of the human R2TP-TTT complex (half maps)

Fileemd_12957_half_map_2.map
AnnotationCryo-EM structure of the human R2TP-TTT complex (half maps)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adapto...

EntireName: RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adaptor proteins
Components
  • Complex: RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adaptor proteins

-
Supramolecule #1: RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adapto...

SupramoleculeName: RUVBL1-RUVBL2-RPAP3-PIH1D1 in complex with TELO2-TTI1-TTI2 adaptor proteins
type: complex / ID: 1 / Parent: 0
Details: The complex was reconstituted using purified proteins from E.coli and Sf9 cells
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 800 kDa/nm

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
140.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 287.15 K / Instrument: LEICA PLUNGER / Details: 3Sec blotting time.
DetailsThis sample was gel filtered

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 100.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 10 / Number real images: 2400 / Average exposure time: 9.0 sec. / Average electron dose: 60.17 e/Å2 / Details: Data was collected in movie mode with 40 fractions
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 168882
CTF correctionSoftware - Name: RELION (ver. 3.0) / Software - details: CTFFIND
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: RELION / Number images used: 90575
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) / Software - details: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0) / Software - details: RELION
Final 3D classificationNumber classes: 3 / Avg.num./class: 44 / Software - Name: RELION (ver. 3.1) / Software - details: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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