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- PDB-3j02: Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state -

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Basic information

Entry
Database: PDB / ID: 3j02
TitleLidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
ComponentsLidless D386A Mm-cpn variant
KeywordsCHAPERONE / Mm-cpn / Chaperonin / ATP-bound
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion 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 ...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. / Ma, B. / DiMaio, F. / Douglas, N.R. / Joachimiak, L. / Baker, D. / Frydman, J. / Levitt, M. / Chiu, W.
CitationJournal: Structure / Year: 2011
Title: Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
Authors: Junjie Zhang / Boxue Ma / Frank DiMaio / Nicholai R Douglas / Lukasz A Joachimiak / David Baker / Judith Frydman / Michael Levitt / Wah Chiu /
Abstract: Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the ...Chaperonins are large ATP-driven molecular machines that mediate cellular protein folding. Group II chaperonins use their "built-in lid" to close their central folding chamber. Here we report the structure of an archaeal group II chaperonin in its prehydrolysis ATP-bound state at subnanometer resolution using single particle cryo-electron microscopy (cryo-EM). Structural comparison of Mm-cpn in ATP-free, ATP-bound, and ATP-hydrolysis states reveals that ATP binding alone causes the chaperonin to close slightly with a ∼45° counterclockwise rotation of the apical domain. The subsequent ATP hydrolysis drives each subunit to rock toward the folding chamber and to close the lid completely. These motions are attributable to the local interactions of specific active site residues with the nucleotide, the tight couplings between the apical and intermediate domains within the subunit, and the aligned interactions between two subunits across the rings. This mechanism of structural changes in response to ATP is entirely different from those found in group I chaperonins.
History
DepositionFeb 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jul 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 1.4Feb 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: Lidless D386A Mm-cpn variant
B: Lidless D386A Mm-cpn variant
C: Lidless D386A Mm-cpn variant
D: Lidless D386A Mm-cpn variant
E: Lidless D386A Mm-cpn variant
F: Lidless D386A Mm-cpn variant
G: Lidless D386A Mm-cpn variant
H: Lidless D386A Mm-cpn variant
I: Lidless D386A Mm-cpn variant
J: Lidless D386A Mm-cpn variant
K: Lidless D386A Mm-cpn variant
L: Lidless D386A Mm-cpn variant
M: Lidless D386A Mm-cpn variant
N: Lidless D386A Mm-cpn variant
O: Lidless D386A Mm-cpn variant
P: Lidless D386A Mm-cpn variant


Theoretical massNumber of molelcules
Total (without water)841,19216
Polymers841,19216
Non-polymers00
Water00
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
Lidless D386A Mm-cpn variant


Mass: 52574.527 Da / Num. of mol.: 16 / Fragment: Lidless Mm-cpn / Mutation: D386A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / 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 D386A Mm-cpn variant / Type: COMPLEX / Details: Methanococcus maripaludis chaperonin
Molecular weightValue: 1 MDa / Experimental value: NO
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FS / Date: Sep 8, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Calibrated magnification: 112000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Gatan side entry / 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 / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: EMAN / Category: 3D reconstruction
CTF correctionDetails: Each CCD image
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionMethod: projection matching / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 12761 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms58591 0 0 0 58591

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