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- EMDB-3414: Structures of human peroxiredoxin 3 suggest self-chaperoning asse... -

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Basic information

Entry
Database: EMDB / ID: EMD-3414
TitleStructures of human peroxiredoxin 3 suggest self-chaperoning assembly that maintains catalytic state
Map dataReconstruction of Human Peroxiredoxin3 filaments formed at pH 4
Sample
  • Sample: Human peroxiredoxin-3 filament
  • Protein or peptide: Peroxiredoxin-3
Function / homology
Function and homology information


NADH-dependent peroxiredoxin activity / negative regulation of kinase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / cell redox homeostasis / regulation of mitochondrial membrane potential ...NADH-dependent peroxiredoxin activity / negative regulation of kinase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / cell redox homeostasis / regulation of mitochondrial membrane potential / cellular response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrion organization / response to hydrogen peroxide / positive regulation of NF-kappaB transcription factor activity / response to oxidative stress / cellular response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 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 peroxide reductase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsYewdall AN / Venugopal HP / Desfosses A / Abrishami V / Yosaatmadja Y / Hampton MB / Gerrard JA / Goldstone D / Mitra AK / Mazdak Radjainia M
CitationJournal: Structure / Year: 2016
Title: Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State.
Authors: N Amy Yewdall / Hariprasad Venugopal / Ambroise Desfosses / Vahid Abrishami / Yuliana Yosaatmadja / Mark B Hampton / Juliet A Gerrard / David C Goldstone / Alok K Mitra / Mazdak Radjainia /
Abstract: Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, ...Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, manifested as quaternary reorganization into a high molecular weight (HMW) form. Acidification, for example, causes dodecameric rings of human peroxiredoxin 3 (HsPrx3) to stack into long helical filaments. In this work, a 4.1-Å resolution structure of low-pH-instigated helical filaments was elucidated, showing a locally unfolded active site and partially folded C terminus. A 2.8-Å crystal structure of HsPrx3 was determined at pH 8.5 under reducing conditions, wherein dodecameric rings are arranged as a short stack, with symmetry similar to low-pH filaments. In contrast to previous observations, the crystal structure displays both a fully folded active site and ordered C terminus, suggesting that the HsPrx3 HMW form maintains catalytic activity. We propose a new role for the HMW form as a self-chaperoning assembly maintaining HsPrx3 function under stress.
History
DepositionApr 15, 2016-
Header (metadata) releaseMay 18, 2016-
Map releaseJun 15, 2016-
UpdateJul 20, 2016-
Current statusJul 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

3414.png

Downloads & links

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Map

FileDownload / File: emd_3414.map.gz / Format: CCP4 / Size: 19.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Human Peroxiredoxin3 filaments formed at pH 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 180 pix.
= 246.96 Å		1.37 Å/pix.
x 170 pix.
= 233.24 Å		1.37 Å/pix.
x 170 pix.
= 233.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-2.32017994 - 6.52894115
Average (Standard dev.)0.11539815 (±0.86083215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170180
Spacing170170180
CellA: 233.23999 Å / B: 233.23999 Å / C: 246.95999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3721.3721.372
M x/y/z170170180
origin x/y/z0.0000.0000.000
length x/y/z233.240233.240246.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170180
D min/max/mean-2.3206.5290.115

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Supplemental data

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Sample components

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Entire : Human peroxiredoxin-3 filament

EntireName: Human peroxiredoxin-3 filament
Components
  • Sample: Human peroxiredoxin-3 filament
  • Protein or peptide: Peroxiredoxin-3

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Supramolecule #1000: Human peroxiredoxin-3 filament

SupramoleculeName: Human peroxiredoxin-3 filament / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Peroxiredoxin-3

MacromoleculeName: Peroxiredoxin-3 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: mitochondria
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant cell: Rosetta / Recombinant plasmid: pET151

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferDetails: 20 mM HEPES, 75 mM NaCl
GridDetails: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 1, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 769 / Average electron dose: 42 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSPRING
Final reconstructionApplied symmetry - Helical parameters - Δz: 42.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 8.7 °
Applied symmetry - Helical parameters - Axial symmetry: D6 (2x6 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: SPRING

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