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- PDB-3iyf: Atomic Model of the Lidless Mm-cpn in the Open State -

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Entry
Database: PDB / ID: 3iyf
TitleAtomic Model of the Lidless Mm-cpn in the Open State
ComponentsChaperonin
KeywordsCHAPERONE / Group II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / 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
Biological speciesMethanococcus maripaludis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsZhang, J. / Baker, M.L. / Schroeder, G. / Douglas, N.R. / Reissmann, S. / Jakana, J. / Dougherty, M. / Fu, C.J. / Levitt, M. / Ludtke, S.J. ...Zhang, 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.
CitationJournal: Nature / Year: 2010
Title: Mechanism of folding chamber closure in a group II chaperonin.
Authors: 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 ...Authors: 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 /
Abstract: Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings ...Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.
History
DepositionOct 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 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
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
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)889,82616
Polymers889,82616
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: D8 (2x8 fold dihedral))

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Components

#1: Protein
Chaperonin / / Chaperonin GroEL (Thermosome / HSP60 family)


Mass: 55614.137 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: hsp60, MMP1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q877G8
Sequence detailsAUTHORS STATE THAT THE LIDLESS MM-CPN IS A MUTANT THAT THE SEQUENCE (I241-K267) HAS BEEN REPLACED ...AUTHORS STATE THAT THE LIDLESS MM-CPN IS A MUTANT THAT THE SEQUENCE (I241-K267) HAS BEEN REPLACED BY A SHORT LINKER (ETASE)

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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: Lidless Mm-cpn / Type: COMPLEX
Details: Lidless Methanococcus maripaludis chaperonin, 16-mer
Molecular weightValue: 0.96 MDa / Experimental value: NO
Buffer solutionName: ATPase buffer / pH: 7.5 / Details: ATPase buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 blot 3 seconds

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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
Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: side-entry / Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 10 eV / Energyfilter lower: 0 eV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: Each micrograph
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionMethod: Projection-match / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms58624 0 0 0 58624

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