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- PDB-4a0v: model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4a0v
Titlemodel refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
DescriptorT-COMPLEX PROTEIN 1 SUBUNIT BETA
KeywordsCHAPERONE / CHAPERONIN / PROTEIN FOLDING
Specimen sourceBos taurus / mammal / CATTLE / ウシ /
MethodElectron microscopy (10.7 A resolution / Single particle / Vitreous ice)
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. / Frydman, J. / Chiu, W.
CitationEMBO J., 2012, 31, 720-730

EMBO J., 2012, 31, 720-730 StrPapers
Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
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

DateDeposition: Sep 13, 2011 / Release: Feb 15, 2012 / Last modification: Aug 12, 2015

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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)881,72516
Polyers881,72516
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Polypeptide(L)
T-COMPLEX PROTEIN 1 SUBUNIT BETA / TCP-1-BETA / CCT-BETA / BOVINE TRIC


Mass: 55107.824 Da / Num. of mol.: 16 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: Q3ZBH0

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

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Sample preparation

Assembly of specimenName: BOVINE TRIC IN THE AMP- PNP STATE / Aggregation state: PARTICLE
Specimen supportDetails: HOLEY CARBON

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Electron microscopy imaging

MicroscopyMicroscope model: OTHER
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: 1200 nm / Cs: 4.1 mm
Specimen holderTemperature: 101 K
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 700
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMAN1.8 / Number of particles: 29374
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 10.7 A / Nominal pixel size: 2.4 A/pix / Actual pixel size: 2.4 A/pix / CTF correction method: EACH MICROGRAPH
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. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1961. (DEPOSITION ID: 10236).
Least-squares processHighest resolution: 10.7 A
Refine hist #LASTHighest resolution: 10.7 A
Number of atoms included #LASTProtein: 59707 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 59707

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