+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1961 | |||||||||
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Title | Symmetry-free cryo-EM map of TRiC-AMP-PNP | |||||||||
Map data | symmetry-free cryo-EM density of TRiC-AMP-PNP | |||||||||
Sample |
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Keywords | TRiC/CCT / chaperonin / cryo-EM / protein folding | |||||||||
Function / homology | Function and homology information Association of TriC/CCT with target proteins during biosynthesis / RHOBTB2 GTPase cycle / RHOBTB1 GTPase cycle / chaperonin-containing T-complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.7 Å | |||||||||
Authors | Cong 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 | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1961.map.gz | 10.3 MB | EMDB map data format | |
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Header (meta data) | emd-1961-v30.xml emd-1961.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_1961.png | 105.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1961 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1961 | HTTPS FTP |
-Validation report
Summary document | emd_1961_validation.pdf.gz | 216.1 KB | Display | EMDB validaton report |
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Full document | emd_1961_full_validation.pdf.gz | 215.2 KB | Display | |
Data in XML | emd_1961_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1961 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1961 | HTTPS FTP |
-Related structure data
Related structure data | 4a0vMC 1960C 1962C 1963C 4a0oC 4a0wC 4a13C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1961.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | symmetry-free cryo-EM density of TRiC-AMP-PNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : bovine TRiC/CCT in the AMP-PNP state
Entire | Name: bovine TRiC/CCT in the AMP-PNP state |
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Components |
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-Supramolecule #1000: bovine TRiC/CCT in the AMP-PNP state
Supramolecule | Name: bovine TRiC/CCT in the AMP-PNP state / type: sample / ID: 1000 / Oligomeric state: 16-mer / Number unique components: 2 |
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Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
-Macromolecule #1: bovine TRiC
Macromolecule | Name: bovine TRiC / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC or CCT / Oligomeric state: 16-mer / Recombinant expression: No |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: bovine |
Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Grid | Details: 200-mesh Quantifoil holey grid |
Vitrification | Cryogen 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 |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Average: 101 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism correction |
Specialist optics | Energy filter - Name: JEOL in-column omega energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 700 / Average electron dose: 18 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry / Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: each micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.7 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: 29374 |