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- EMDB-0496: hTRiC-hPFD all particles -

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Basic information

Entry
Database: EMDB / ID: EMD-0496
TitlehTRiC-hPFD all particles
Map datahTRiC-hPFD all particles
Sample
  • Complex: hTRiC-hPFD
    • Complex: hTRiC
    • Complex: hPFD
Function / homology
Function and homology information


RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / RPAP3/R2TP/prefoldin-like complex / RNA polymerase II core complex assembly / positive regulation of protein localization to Cajal body / tubulin complex assembly ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / RPAP3/R2TP/prefoldin-like complex / RNA polymerase II core complex assembly / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / negative regulation of amyloid fibril formation / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / protein folding chaperone complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / beta-tubulin binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / microtubule-based process / chaperone-mediated protein folding / protein folding chaperone / : / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / tubulin binding / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / negative regulation of canonical Wnt signaling pathway / response to virus / cilium / mRNA 5'-UTR binding / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transcription corepressor activity / G-protein beta-subunit binding / azurophil granule lumen / melanosome / unfolded protein binding / protein folding / retina development in camera-type eye / amyloid-beta binding / cell body / protein-folding chaperone binding / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cadherin binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / T-complex protein 1, alpha subunit ...Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Prefoldin subunit 6 / Prefoldin subunit 1 / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit gamma / T-complex protein 1 subunit theta / T-complex protein 1 subunit delta / Prefoldin subunit 3 / T-complex protein 1 subunit beta ...Prefoldin subunit 6 / Prefoldin subunit 1 / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit gamma / T-complex protein 1 subunit theta / T-complex protein 1 subunit delta / Prefoldin subunit 3 / T-complex protein 1 subunit beta / Prefoldin subunit 5 / T-complex protein 1 subunit eta / Prefoldin subunit 4 / Prefoldin subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsGestaut DR / Roh SH
Funding support United States, Germany, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteR01GM074074 United States
National Institutes of Health/National Human Genome Research InstituteP41GM103832 United States
National Institutes of Health/National Human Genome Research InstituteF32GM103124 United States
National Institutes of Health/National Human Genome Research InstituteP01NS092525 United States
National Institutes of Health/National Human Genome Research InstituteR01GM079429 United States
European Research CouncilAdvG #670821 Germany
European Research CouncilAdvG #233226 Germany
CitationJournal: Cell / Year: 2019
Title: The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis.
Authors: Daniel Gestaut / Soung Hun Roh / Boxue Ma / Grigore Pintilie / Lukasz A Joachimiak / Alexander Leitner / Thomas Walzthoeni / Ruedi Aebersold / Wah Chiu / Judith Frydman /
Abstract: Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the ...Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
History
DepositionJan 23, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseJun 19, 2019-
UpdateJun 19, 2019-
Current statusJun 19, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0496.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhTRiC-hPFD all particles
Voxel sizeX=Y=Z: 1.7 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.061091244 - 0.23372656
Average (Standard dev.)0.00061021233 (±0.0108286785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0610.2340.001

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Supplemental data

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Additional map: hTRiC-hPFD all particles, unfiltered sum map

Fileemd_0496_additional.map
AnnotationhTRiC-hPFD all particles, unfiltered sum map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: hTRiC-hPFD all particles, half map 1

Fileemd_0496_half_map_1.map
AnnotationhTRiC-hPFD all particles, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: hTRiC-hPFD all particles, half map 2

Fileemd_0496_half_map_2.map
AnnotationhTRiC-hPFD all particles, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : hTRiC-hPFD

EntireName: hTRiC-hPFD
Components
  • Complex: hTRiC-hPFD
    • Complex: hTRiC
    • Complex: hPFD

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Supramolecule #1: hTRiC-hPFD

SupramoleculeName: hTRiC-hPFD / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)

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Supramolecule #2: hTRiC

SupramoleculeName: hTRiC / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)

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Supramolecule #3: hPFD

SupramoleculeName: hPFD / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95808
FSC plot (resolution estimation)

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