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- PDB-3ktt: Atomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0... -

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Entry
Database: PDB / ID: 3ktt
TitleAtomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0 Angstrom cryo-EM map
DescriptorT-complex protein 1 subunit beta
KeywordsCHAPERONE / TRiC/CCT / CCT2(beta) / cryo-EM / Acetylation / ATP-binding / Chaperone / Cytoplasm / Nucleotide-binding
Specimen sourceBos taurus / mammal / bovine / ウシ /
MethodElectron microscopy (4 Å resolution / Particle / Single particle)
AuthorsCong, Y. / Baker, M.L. / Ludtke, S.J. / Frydman, J. / Chiu, W.
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972

primary. Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972 Yorodumi Papers
4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
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

#1. To be Published Search PubMed
To be published
Cong, Y. / Baker, M.L. / Jakana, J. / Woolford, D. / Miller, E.J. / Reissmann, S. / Kumar, R.N. / Redding-Johanson, A.M. / Batth, T.S. / Mukhopadhyay, A. / Ludtke, S.J. / Frydman, J. / Chiu, W.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 25, 2009 / Release: Mar 16, 2010
RevisionDateData content typeGroupProviderType
1.0Mar 16, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
B: T-complex protein 1 subunit beta


Theoretical massNumber of molelcules
Total (without water)55,1071
Polyers55,1071
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 55107.234 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: Q3ZBH0

Cellular component

Molecular function

Biological process

  • 'de novo' protein folding (GO: 0006458)
  • binding of sperm to zona pellucida (GO: 0007339)
  • chaperone mediated protein folding independent of cofactor (GO: 0051086)
  • chaperone-mediated protein complex assembly (GO: 0051131)
  • chaperone-mediated protein folding (GO: 0061077)
  • positive regulation of establishment of protein localization to telomere (GO: 1904851)
  • positive regulation of protein localization to Cajal body (GO: 1904871)
  • positive regulation of telomerase activity (GO: 0051973)
  • positive regulation of telomerase RNA localization to Cajal body (GO: 1904874)
  • positive regulation of telomere maintenance via telomerase (GO: 0032212)
  • protein stabilization (GO: 0050821)
  • scaRNA localization to Cajal body (GO: 0090666)
  • toxin transport (GO: 1901998)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: CCT2(beta) subunit in the both-ring closed bovine TRiC complex
Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Details: vitrification using ethane as cryogen

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Aug 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm
Specimen holderTemperature: 101 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1CootMODEL FITTING
2ModellerMODEL FITTING
3UCSF ChimeraMODEL FITTING
4EMANRECONSTRUCTION
CTF correctionDetails: FSC at 0.5 cut-off
SymmetryPoint symmetry: C2
3D reconstructionMethod: Projection matching / Resolution: 4 Å / Number of particles: 101000 / Actual pixel size: 1.2
Details: Single particle 3D reconstruction using EMAN1.8+ with our recently developed 2-D fast rotation matching method (FRM2D) for the image alignment.
Symmetry type: POINT
Atomic model buildingDetails: METHOD--Local refinement, Flexible fitting REFINEMENT PROTOCOL--Local refinement, Flexible fitting
Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingDetails: Homology model
Number of atoms included #LASTProtein: 3855 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3855

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