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- PDB-6e0g: Mitochondrial peroxiredoxin from Leishmania infantum after heat s... -

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Basic information

Entry
Database: PDB / ID: 6e0g
TitleMitochondrial peroxiredoxin from Leishmania infantum after heat stress without unfolding client protein
Componentsmitochondrial 2-cys-peroxiredoxin
KeywordsCHAPERONE / heat-shock / client-binding / holdase / unfolding
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to stress / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTeixeira, F. / Tse, E. / Makepeace, K.A.T. / Borchers, C.H. / Castro, H. / Tomas, A.M. / Poole, L.B. / Southworth, D.R. / Jakob, U.
CitationJournal: Nat Commun / Year: 2019
Title: Chaperone activation and client binding of a 2-cysteine peroxiredoxin.
Authors: Filipa Teixeira / Eric Tse / Helena Castro / Karl A T Makepeace / Ben A Meinen / Christoph H Borchers / Leslie B Poole / James C Bardwell / Ana M Tomás / Daniel R Southworth / Ursula Jakob /
Abstract: Many 2-Cys-peroxiredoxins (2-Cys-Prxs) are dual-function proteins, either acting as peroxidases under non-stress conditions or as chaperones during stress. The mechanism by which 2-Cys-Prxs switch ...Many 2-Cys-peroxiredoxins (2-Cys-Prxs) are dual-function proteins, either acting as peroxidases under non-stress conditions or as chaperones during stress. The mechanism by which 2-Cys-Prxs switch functions remains to be defined. Our work focuses on Leishmania infantum mitochondrial 2-Cys-Prx, whose reduced, decameric subpopulation adopts chaperone function during heat shock, an activity that facilitates the transition from insects to warm-blooded host environments. Here, we have solved the cryo-EM structure of mTXNPx in complex with a thermally unfolded client protein, and revealed that the flexible N-termini of mTXNPx form a well-resolved central belt that contacts and encapsulates the unstructured client protein in the center of the decamer ring. In vivo and in vitro cross-linking studies provide further support for these interactions, and demonstrate that mTXNPx decamers undergo temperature-dependent structural rearrangements specifically at the dimer-dimer interfaces. These structural changes appear crucial for exposing chaperone-client binding sites that are buried in the peroxidase-active protein.
History
DepositionJul 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
J: mitochondrial 2-cys-peroxiredoxin
A: mitochondrial 2-cys-peroxiredoxin
B: mitochondrial 2-cys-peroxiredoxin
C: mitochondrial 2-cys-peroxiredoxin
D: mitochondrial 2-cys-peroxiredoxin
E: mitochondrial 2-cys-peroxiredoxin
F: mitochondrial 2-cys-peroxiredoxin
G: mitochondrial 2-cys-peroxiredoxin
H: mitochondrial 2-cys-peroxiredoxin
I: mitochondrial 2-cys-peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)254,00110
Polymers254,00110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
mitochondrial 2-cys-peroxiredoxin


Mass: 25400.131 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: mTXNPx, LINJ_23_0050 / Production host: Escherichia coli (E. coli)
References: UniProt: Q95U89, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases

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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: reduced decamer form of a 2-cys peroxiredoxin after heat stress
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: YES
Source (natural)Organism: Leishmania infantum (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 48450 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2368
Image scansWidth: 3838 / Height: 3710

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386653 / Symmetry type: POINT

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