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- EMDB-1962: Symmetry-free cryo-EM map of TRiC-ADP-AlFx -

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Basic information

Entry
Database: EMDB / ID: EMD-1962
TitleSymmetry-free cryo-EM map of TRiC-ADP-AlFx
Map datasymmetry-free cryo-EM density map of TRiC-ADP-AlFx
Sample
  • Sample: bovine TRiC/CCT
  • Protein or peptide: bovine TRiC
KeywordsTRiC/CCT / chaperonin / cryo-EM / protein folding / ATP-driven conformational change
Function / homology
Function and homology information


Association of TriC/CCT with target proteins during biosynthesis / RHOBTB1 GTPase cycle / RHOBTB2 GTPase cycle / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / chaperonin-containing T-complex / positive regulation of telomerase RNA localization to Cajal body / binding of sperm to zona pellucida ...Association of TriC/CCT with target proteins during biosynthesis / RHOBTB1 GTPase cycle / RHOBTB2 GTPase cycle / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / chaperonin-containing T-complex / positive regulation of telomerase RNA localization to Cajal body / binding of sperm to zona pellucida / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / chaperone-mediated protein complex assembly / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cell body / microtubule / protein stabilization / ubiquitin protein ligase binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
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
T-complex protein 1 subunit beta
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.9 Å
AuthorsCong Y / Schroder GF / Meyer AS / Jakana J / Ma B / Dougherty MT / Schmid MF / Reissmann S / Levitt M / Ludtke SL ...Cong Y / Schroder GF / Meyer AS / Jakana J / Ma B / Dougherty MT / Schmid MF / Reissmann S / Levitt M / Ludtke SL / Frydman J / Chiu W
CitationJournal: EMBO J / Year: 2012
Title: Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
Authors: Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu /
Abstract: The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered ...The eukaryotic group II chaperonin TRiC/CCT is a 16-subunit complex with eight distinct but similar subunits arranged in two stacked rings. Substrate folding inside the central chamber is triggered by ATP hydrolysis. We present five cryo-EM structures of TRiC in apo and nucleotide-induced states without imposing symmetry during the 3D reconstruction. These structures reveal the intra- and inter-ring subunit interaction pattern changes during the ATPase cycle. In the apo state, the subunit arrangement in each ring is highly asymmetric, whereas all nucleotide-containing states tend to be more symmetrical. We identify and structurally characterize an one-ring closed intermediate induced by ATP hydrolysis wherein the closed TRiC ring exhibits an observable chamber expansion. This likely represents the physiological substrate folding state. Our structural results suggest mechanisms for inter-ring-negative cooperativity, intra-ring-positive cooperativity, and protein-folding chamber closure of TRiC. Intriguingly, these mechanisms are different from other group I and II chaperonins despite their similar architecture.
History
DepositionSep 5, 2011-
Header (metadata) releaseFeb 6, 2012-
Map releaseFeb 6, 2012-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4a0w
  • Surface level: 1
  • 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_1962.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetry-free cryo-EM density map of TRiC-ADP-AlFx
Voxel sizeX=Y=Z: 2.4 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.02576828 - 1.50151169
Average (Standard dev.)0.05718635 (±0.23651719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-1.0261.5020.057

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Supplemental data

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Sample components

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Entire : bovine TRiC/CCT

EntireName: bovine TRiC/CCT
Components
  • Sample: bovine TRiC/CCT
  • Protein or peptide: bovine TRiC

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Supramolecule #1000: bovine TRiC/CCT

SupramoleculeName: bovine TRiC/CCT / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 2
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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Macromolecule #1: bovine TRiC

MacromoleculeName: bovine TRiC / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC or CCT / Oligomeric state: 16-mer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

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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

Concentration1 mg/mL
GridDetails: 200-mesh Quantifoil holey grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: FEI vitrobot / Method: Two-side blotting for 1 second before plunging

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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 / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: JEOL in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureAverage: 101 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism correction
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 300 / Average electron dose: 18 e/Å2
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1.8
Details: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps
Number images used: 16495

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