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- PDB-3iyg: Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map -

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Basic information

Entry
Database: PDB / ID: 3iyg
TitleCa model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
Components
  • (T-complex protein 1 subunit ...) x 7
  • T-complex protein 1 subunit
KeywordsCHAPERONE / TRiC/CCT / Asymmetric / Cryo-EM / subunit arrangement / ATP-binding / Isopeptide bond / Nucleotide-binding / Phosphoprotein / Disulfide bond
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 / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / cilium / melanosome / unfolded protein binding / protein folding / cell body / microtubule / protein stabilization / centrosome / ubiquitin protein ligase binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
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, beta subunit / Chaperonins TCP-1 signature 1. / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site ...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, 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 eta / T-complex protein 1 subunit delta / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit beta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsCong, Y. / Baker, M.L. / Ludtke, S.J. / Frydman, J. / Chiu, W.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
Authors: Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / ...Authors: Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / Steven J Ludtke / Judith Frydman / Wah Chiu /
Abstract: The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates ...The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.
History
DepositionNov 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Assembly

Deposited unit
Q: T-complex protein 1 subunit theta
G: T-complex protein 1 subunit gamma
Z: T-complex protein 1 subunit zeta
D: T-complex protein 1 subunit delta
B: T-complex protein 1 subunit beta
E: T-complex protein 1 subunit
A: T-complex protein 1 subunit alpha
H: T-complex protein 1 subunit eta


Theoretical massNumber of molelcules
Total (without water)451,9498
Polymers451,9498
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: D8 (2x8 fold dihedral))

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Components

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T-complex protein 1 subunit ... , 7 types, 7 molecules QGZDBAH

#1: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta / Coordinate model: Cα atoms only


Mass: 55833.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZCI9
#2: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / Coordinate model: Cα atoms only


Mass: 57486.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0K2
#3: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta / CCT-zeta-1 / Coordinate model: Cα atoms only


Mass: 56602.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHL7
#4: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Coordinate model: Cα atoms only


Mass: 56057.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2T9X2
#5: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta / Coordinate model: Cα atoms only


Mass: 55107.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBH0
#7: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha / Coordinate model: Cα atoms only


Mass: 57495.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32L40
#8: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / Coordinate model: Cα atoms only


Mass: 56614.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2NKZ1

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Protein , 1 types, 1 molecules E

#6: Protein T-complex protein 1 subunit / Coordinate model: Cα atoms only


Mass: 56751.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)

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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 (also called CCT) / Type: COMPLEX
Molecular weightValue: 1 MDa / Experimental value: NO
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Temp: 101 K / Humidity: 95 % / Details: vitrification using ethane as cryogen / Method: two-side blotting for 1 second before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Aug 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm / Astigmatism: objective lens astigmatism correction / Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: side entry / Temperature: 101 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2MODELLERmodel fitting
3UCSF Chimeramodel fitting
4EMAN3D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: Projection matching / Resolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 101000 / Nominal pixel size: 1.2 Å / Actual pixel size: 1.2 Å
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 ( Details about the particle: A recently ...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 ( Details about the particle: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps )
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--Local refinement, Flexible fitting REFINEMENT PROTOCOL--Local refinement, Flexible fitting
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 0 0 4134

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