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- PDB-8pe8: Symmetry expanded D7 local refined map of mitochondrial heat-shoc... -

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Basic information

Entry
Database: PDB / ID: 8pe8
TitleSymmetry expanded D7 local refined map of mitochondrial heat-shock protein 60-like protein from Chaetomium thermophilum
ComponentsMitochondrial heat shock protein 60-like protein
KeywordsCHAPERONE / mitochondrial heat-shock protein 60-like protein / Stress response / ATP-binding / Nucleotide-binding / Chaetomium thermophilum / native cell extracts
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / protein refolding / ATP binding
Similarity search - Function
Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / 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
Mitochondrial heat shock protein 60-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsSemchonok, D.A. / Kyrilis, F.L. / Hamdi, F. / Kastritis, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Symmetry expanded D7, locally refined cryo-EM map of mitochondrial heat shock protein 60-like protein Chaetomium thermophilum.
Authors: Semchonok, D.A. / Kyrilis, F.L. / Hamdi, F. / Kastritis, P.L.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial heat shock protein 60-like protein
B: Mitochondrial heat shock protein 60-like protein
C: Mitochondrial heat shock protein 60-like protein
D: Mitochondrial heat shock protein 60-like protein
E: Mitochondrial heat shock protein 60-like protein
F: Mitochondrial heat shock protein 60-like protein
G: Mitochondrial heat shock protein 60-like protein
H: Mitochondrial heat shock protein 60-like protein
I: Mitochondrial heat shock protein 60-like protein
J: Mitochondrial heat shock protein 60-like protein
K: Mitochondrial heat shock protein 60-like protein
L: Mitochondrial heat shock protein 60-like protein
M: Mitochondrial heat shock protein 60-like protein
N: Mitochondrial heat shock protein 60-like protein


Theoretical massNumber of molelcules
Total (without water)849,37314
Polymers849,37314
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47220 Å2
ΔGint-201 kcal/mol
Surface area323630 Å2

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Components

#1: Protein
Mitochondrial heat shock protein 60-like protein


Mass: 60669.473 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYB3

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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: native cell extract of Chaetomium thermophilum / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Purified and fractionated (fraction 25) cell lysate of Chaetomium thermophilum
Entity ID: all / Source: NATURAL
Molecular weightValue: 0.06 MDa / Experimental value: NO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Buffer solutionpH: 7.4
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 28 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1109
EM imaging opticsPhase plate: OTHER

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2particle selection
3Gctf1.18CTF correction
6Coot0.9.8.1 ELmodel fittingmanual refinement
8EPUimage acquisition
9PHENIX1.20.1-4487model refinementReal-space refinement
10cryoSPARC3.2initial Euler assignment
11cryoSPARC3.2final Euler assignment
12cryoSPARC3.2classification
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 287314
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15942 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingAccession code: G0RYB3
Details: The initial model consisted of the complete monomeric unit of HSP60
Source name: AlphaFold / Type: in silico model

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