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- PDB-4a0o: Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state -

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Basic information

Entry
Database: PDB / ID: 4a0o
TitleSymmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
ComponentsT-COMPLEX PROTEIN 1 SUBUNIT BETA
KeywordsCHAPERONE / CHAPERONIN / 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
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 ...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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsCong, Y. / Schroder, G.F. / Meyer, A.S. / Jakana, J. / Ma, B. / Dougherty, M.T. / Schmid, M.F. / Reissmann, S. / Levitt, M. / Ludtke, S.L. ...Cong, Y. / Schroder, G.F. / Meyer, A.S. / Jakana, J. / Ma, B. / Dougherty, M.T. / Schmid, M.F. / Reissmann, S. / Levitt, M. / Ludtke, S.L. / 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 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Apr 19, 2017Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-1960
  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: T-COMPLEX PROTEIN 1 SUBUNIT BETA
B: T-COMPLEX PROTEIN 1 SUBUNIT BETA
C: T-COMPLEX PROTEIN 1 SUBUNIT BETA
D: T-COMPLEX PROTEIN 1 SUBUNIT BETA
E: T-COMPLEX PROTEIN 1 SUBUNIT BETA
F: T-COMPLEX PROTEIN 1 SUBUNIT BETA
G: T-COMPLEX PROTEIN 1 SUBUNIT BETA
H: T-COMPLEX PROTEIN 1 SUBUNIT BETA
I: T-COMPLEX PROTEIN 1 SUBUNIT BETA
J: T-COMPLEX PROTEIN 1 SUBUNIT BETA
K: T-COMPLEX PROTEIN 1 SUBUNIT BETA
L: T-COMPLEX PROTEIN 1 SUBUNIT BETA
M: T-COMPLEX PROTEIN 1 SUBUNIT BETA
N: T-COMPLEX PROTEIN 1 SUBUNIT BETA
O: T-COMPLEX PROTEIN 1 SUBUNIT BETA
P: T-COMPLEX PROTEIN 1 SUBUNIT BETA


Theoretical massNumber of molelcules
Total (without water)881,71616
Polymers881,71616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
T-COMPLEX PROTEIN 1 SUBUNIT BETA / TRIC/CCT / TCP-1-BETA / CCT-BETA / BOVINE TRIC


Mass: 55107.234 Da / Num. of mol.: 16 / Fragment: RESIDUES 14-526 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: TESTES / References: UniProt: Q3ZBH0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BOVINE TRIC IN THE NUCLEOTIDE FREE STATE / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHEN

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Oct 20, 2008 / Details: NONE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Specimen holderTemperature: 101 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 700

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Processing

EM softwareName: DireX / Category: model fitting
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.5 Å / Num. of particles: 47151 / Nominal pixel size: 2.4 Å / Actual pixel size: 2.4 Å
Details: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE ...Details: OUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS, BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. WE FITTED THE MODEL WITH THE OCCUPANCY REFINEMENT FEATURE IN DIREX. THIS BASICALLY DETERMINES WHETHER THERE IS SUFFICIENT DENSITY FOR EACH RESIDUE OR IF THERE IS REDUCED OR MISSING DENSITY. THE OCCUPANCY IS VALUE BETWEEN 0 AND 1. WE WROTE THIS VALUE INTO THE B-FACTOR COLUMN AS 100X(1-OCCUPANCY). THIS RESEMBLES A B-FACTOR BUT IS NOT EXACTLY THE SAME. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1960. (DEPOSITION ID: 10235).
Symmetry type: POINT
RefinementHighest resolution: 10.5 Å
Refinement stepCycle: LAST / Highest resolution: 10.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56830 0 0 0 56830

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