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- EMDB-8947: Mitochondrial peroxiredoxin from Leishmania infantum after heat s... -

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Basic information

Entry
Database: EMDB / ID: EMD-8947
TitleMitochondrial peroxiredoxin from Leishmania infantum after heat stress without unfolding client protein
Map dataMitochondrial peroxiredoxin from Leishmania infantum after heat stress without unfolding client protein - primary map
Sample
  • Complex: reduced decamer form of a 2-cys peroxiredoxin 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: 2.9 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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e0g
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8947.png

Downloads & links

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Map

FileDownload / File: emd_8947.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMitochondrial peroxiredoxin from Leishmania infantum after heat stress without unfolding client protein - primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 180 pix.
= 185.76 Å		1.03 Å/pix.
x 180 pix.
= 185.76 Å		1.03 Å/pix.
x 180 pix.
= 185.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.1
Minimum - Maximum-0.5511869 - 0.7765474
Average (Standard dev.)0.00097394985 (±0.02943495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 185.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0321.0321.032
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z185.760185.760185.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.5510.7770.001

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Supplemental data

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Sample components

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Entire : reduced decamer form of a 2-cys peroxiredoxin after heat stress

EntireName: reduced decamer form of a 2-cys peroxiredoxin after heat stress
Components
  • Complex: reduced decamer form of a 2-cys peroxiredoxin after heat stress
    • Protein or peptide: mitochondrial 2-cys-peroxiredoxin

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Supramolecule #1: reduced decamer form of a 2-cys peroxiredoxin after heat stress

SupramoleculeName: reduced decamer form of a 2-cys peroxiredoxin 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: 2368 / 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: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 48450
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 386653
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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