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Yorodumi- PDB-6e0g: Mitochondrial peroxiredoxin from Leishmania infantum after heat s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e0g | ||||||
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Title | Mitochondrial peroxiredoxin from Leishmania infantum after heat stress without unfolding client protein | ||||||
Components | mitochondrial 2-cys-peroxiredoxin | ||||||
Keywords | CHAPERONE / heat-shock / client-binding / holdase / unfolding | ||||||
Function / homology | Function and homology information thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / response to oxidative stress / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Leishmania infantum (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Teixeira, F. / Tse, E. / Makepeace, K.A.T. / Borchers, C.H. / Castro, H. / Tomas, A.M. / Poole, L.B. / Southworth, D.R. / Jakob, U. | ||||||
Citation | Journal: 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 |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6e0g.cif.gz | 290.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e0g.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 6e0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e0g_validation.pdf.gz | 950.2 KB | Display | wwPDB validaton report |
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Full document | 6e0g_full_validation.pdf.gz | 968 KB | Display | |
Data in XML | 6e0g_validation.xml.gz | 50.2 KB | Display | |
Data in CIF | 6e0g_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/6e0g ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e0g | HTTPS FTP |
-Related structure data
Related structure data | 8947MC 8946C 6e0fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: reduced decamer form of a 2-cys peroxiredoxin after heat stress Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: YES |
Source (natural) | Organism: Leishmania infantum (eukaryote) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 48450 X / Nominal defocus max: 2100 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2368 |
Image scans | Width: 3838 / Height: 3710 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: D5 (2x5 fold dihedral) |
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386653 / Symmetry type: POINT |