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- EMDB-8946: Mitochondrial peroxiredoxin from Leishmania infantum in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-8946
TitleMitochondrial peroxiredoxin from Leishmania infantum in complex with unfolding client protein after heat stress
Map datastructure of mitochondrial peroxiredoxin from Leishmania infantum adopting chaperone function in complex with unfolding client protein
Sample
  • Complex: Chaperone complex of a 2-cys peroxiredoxin binding to unfolded client protein luciferase after heat stress
    • Protein or peptide: mitochondrial 2-cys-peroxiredoxin
Keywordsheat-shock / client-binding / holdase / unfolding / CHAPERONE
Function / homology
Function and homology information


peroxiredoxin activity / thioredoxin-dependent peroxiredoxin
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTeixeira F / Tse E
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, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseFeb 20, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e0f
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8946.png

Downloads & links

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Map

FileDownload / File: emd_8946.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of mitochondrial peroxiredoxin from Leishmania infantum adopting chaperone function in complex with unfolding client protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 180 pix.
= 180. Å		1 Å/pix.
x 180 pix.
= 180. Å		1 Å/pix.
x 180 pix.
= 180. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0341 / Movie #1: 0.045
Minimum - Maximum-0.19447628 - 0.2933862
Average (Standard dev.)0.0015930015 (±0.013635578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 180.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z180.000180.000180.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1940.2930.002

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Supplemental data

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Sample components

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Entire : Chaperone complex of a 2-cys peroxiredoxin binding to unfolded cl...

EntireName: Chaperone complex of a 2-cys peroxiredoxin binding to unfolded client protein luciferase after heat stress
Components
  • Complex: Chaperone complex of a 2-cys peroxiredoxin binding to unfolded client protein luciferase after heat stress
    • Protein or peptide: mitochondrial 2-cys-peroxiredoxin

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Supramolecule #1: Chaperone complex of a 2-cys peroxiredoxin binding to unfolded cl...

SupramoleculeName: Chaperone complex of a 2-cys peroxiredoxin binding to unfolded client protein luciferase after heat stress
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leishmania infantum (eukaryote)

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Macromolecule #1: mitochondrial 2-cys-peroxiredoxin

MacromoleculeName: mitochondrial 2-cys-peroxiredoxin / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
Source (natural)Organism: Leishmania infantum (eukaryote)
Molecular weightTheoretical: 25.400131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLRRLPTSCF LKRSQFRGFA ATSPLLNLDY QMYRTATVRE AAPQFSGQAV VNGAIKDINM NDYKGKYIVL FFYPMDFTFV CPTEIIAFS DRHADFEKLN TQVVAVSCDS VYSHLAWVNT PRKKGGLGEM HIPVLADKSM EIARDYGVLI EESGIALRGL F IIDKKGIL ...String:
MLRRLPTSCF LKRSQFRGFA ATSPLLNLDY QMYRTATVRE AAPQFSGQAV VNGAIKDINM NDYKGKYIVL FFYPMDFTFV CPTEIIAFS DRHADFEKLN TQVVAVSCDS VYSHLAWVNT PRKKGGLGEM HIPVLADKSM EIARDYGVLI EESGIALRGL F IIDKKGIL RHSTINDLPV GRNVDEALRV LEAFQYADEN GDAIPCGWKP GQPTLDTTKA GEFFEKNM

UniProtKB: thioredoxin-dependent peroxiredoxin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number real images: 2810 / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4kb3

Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213512
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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