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- PDB-3los: Atomic Model of Mm-cpn in the Closed State -

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Entry
Database: PDB / ID: 3los
TitleAtomic Model of Mm-cpn in the Closed State
DescriptorChaperonin
KeywordsCHAPERONE / Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone / ATP-binding / Nucleotide-binding
Specimen sourceMethanococcus maripaludis / archaea / メタノコッカス・マリパルディス
MethodElectron microscopy (4.3 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsZhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. / Frydman, J. / Chiu, W.
CitationNature, 2010, 463, 379-383

Nature, 2010, 463, 379-383 StrPapers
Mechanism of folding chamber closure in a group II chaperonin.
Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu

DateDeposition: Feb 4, 2010 / Release: Mar 16, 2010

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Assembly

Deposited unit
A: Chaperonin
B: Chaperonin
C: Chaperonin
D: Chaperonin
E: Chaperonin
F: Chaperonin
G: Chaperonin
H: Chaperonin
I: Chaperonin
J: Chaperonin
K: Chaperonin
L: Chaperonin
M: Chaperonin
N: Chaperonin
O: Chaperonin
P: Chaperonin


Theoretical massNumber of molelcules
Total (without water)932,65316
Polyers932,65316
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
Chaperonin / Chaperonin GroEL (Thermosome / HSP60 family)


Mass: 58290.793 Da / Num. of mol.: 16
Source: (gene. exp.) Methanococcus maripaludis / archaea / メタノコッカス・マリパルディス
References: UniProt: Q877G8

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: Mm-cpn with 1mM ATP/AlFx / Aggregation state: PARTICLE / Composition: 16-mer / Mol wt exp: 0.96 MDa / Mol wt theo: 0.96 MDa / Number of components: 1
ComponentName: Methanococcus maripaludis chaperonin / Type: PROTEIN
Buffer solutionName: ATPase buffer
Sample preparationpH: 7.5
VitrificationInstrument: Vitrobot / Cryogen name: ETHANE / Humidity: 100 / Method: 1 blot 3 seconds

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Electron microscopy imaging

EM imagingCamera length: 0 mm
MicroscopyMicroscope model: JEM3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 112000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Energy filter: in column omega filter / Energy window: 0-10
Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: side-entry / Temperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Gatan 4kX4k CCD Camera
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM single particle entitySymmetry type: DIHEDRAL
3D reconstructionMethod: Projection-match / Software: EMAN / Resolution: 4.3 A / Resolution method: FSC at 0.5 cut-off / CTF correction method: Each micrograph
Details: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
Atomic model buildingDetails: THE SINGLE SUBUNIT MODEL OF MM-CPN WAS MANUALLY BUILT IN THE CRYO-EM DENSITY USING COOT. THE ENTIRE 16-SUBUNIT COMPLEX WAS GENERATED BASED ON THE D8 SYMMETRY.
Number of atoms included #LASTProtein: 63712 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 63712

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