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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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Entry
Database: PDB / ID: 3iyg
TitleCa model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
DescriptorT-complex protein 1 subunit theta
T-complex protein 1 subunit gamma
T-complex protein 1 subunit zeta
T-complex protein 1 subunit delta
T-complex protein 1 subunit beta
T-complex protein 1 subunit alpha
T-complex protein 1 subunit eta
KeywordsCHAPERONE / TRiC/CCT / Asymmetric / Cryo-EM / subunit arrangement / ATP-binding / Chaperone / Isopeptide bond / Nucleotide-binding / Phosphoprotein / Disulfide bond
Specimen sourceBos taurus / mammal / bovine / ウシ /
MethodElectron microscopy (4 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsCong, Y. / Baker, M.L. / Ludtke, S.J. / Frydman, J. / Chiu, W.
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972

Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972 StrPapers
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

DateDeposition: Nov 28, 2009 / Release: Mar 16, 2010 / Last modification: Apr 7, 2010

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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)451,9548
Polyers451,9548
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polypeptide(L) , 8 types, 8 molecules QGZDBEAH

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


Mass: 55834.520 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3ZCI9

Cellular component

Molecular function

Biological process

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


Mass: 57486.820 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3T0K2

Cellular component

Molecular function

Biological process

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


Mass: 56602.930 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3MHL7

Cellular component

Molecular function

Biological process

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


Mass: 56058.527 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q2T9X2

Cellular component

Molecular function

Biological process

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


Mass: 55107.824 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3ZBH0

Cellular component

Molecular function

Biological process

  • binding of sperm to zona pellucida (GO: 0007339)
  • chaperone mediated protein folding independent of cofactor (GO: 0051086)
  • chaperone-mediated protein complex assembly (GO: 0051131)
  • 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)
#6: Polypeptide(L)T-complex protein 1 subunit


Mass: 56752.227 Da / Num. of mol.: 1 / Source: (natural) Bos taurus
#7: Polypeptide(L)T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


Mass: 57495.941 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q32L40

Cellular component

Molecular function

Biological process

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


Mass: 56614.812 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q2NKZ1

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: bovine TRiC (also called CCT) / Aggregation state: PARTICLE / Mol wt exp: 1 MDa / Mol wt theo: 1 MDa / Number of components: 8
ComponentName: TRiC (also called CCT) / Type: PROTEIN
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

EM imagingCamera length: 0 mm
MicroscopyMicroscope model: JEM3200FSC / Date: Aug-2007 to Aug-2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm / Astigmatism: objective lens astigmatism correction / Energy filter: in-column omega energy filter / Energy window: 0-20
Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: side entry / Temperature: 101 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Kodak SO163 film
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: COOT, Chimera, Modeller
3D reconstructionMethod: Projection matching / Software: EMAN / Resolution: 4 A / Resolution method: FSC at 0.5 cut-off / Number of particles: 101000 / Nominal pixel size: 1.2 A/pix / Actual pixel size: 1.2 A/pix / CTF correction method: each micrograph
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 )
Atomic model buildingMethod: Local refinement, Flexible fitting / Software name: COOT, Chimera, Modeller / Ref protocol: Local refinement, Flexible fitting / Ref space: REAL
Number of atoms included #LASTProtein: 4134 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4134

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