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- EMDB-6309: Cryo-EM structure of human peroxiredoxin-3 filament reveals the a... -

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Basic information

Entry
Database: EMDB / ID: EMD-6309
TitleCryo-EM structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone
Map dataCryo-EM structure of human peroxiredoxin-3 filament
Sample
  • Sample: Human peroxiredoxin-3 filament
  • Protein or peptide: Peroxiredoxin 3
KeywordsPeroxiredoxin / 2-Cys Prx high-molecular-weight form / cryo-electron microscopy / image processing / molecular chaperone
Function / homology
Function and homology information


peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrion organization ...peptidyl-cysteine oxidation / alkyl hydroperoxide reductase activity / maternal placenta development / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / myeloid cell differentiation / negative regulation of kinase activity / Detoxification of Reactive Oxygen Species / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrion organization / cell redox homeostasis / regulation of mitochondrial membrane potential / hydrogen peroxide catabolic process / response to hydrogen peroxide / cellular response to reactive oxygen species / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / response to oxidative stress / response to lipopolysaccharide / early endosome / mitochondrial matrix / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsRadjainia M / Venugopal HP / Desfosses A / Phillips AJ / Yewdall NA / Hampton MB / Gerrard JA / Mitra AK
CitationJournal: Structure / Year: 2015
Title: Cryo-electron microscopy structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone.
Authors: Mazdak Radjainia / Hariprasad Venugopal / Ambroise Desfosses / Amy J Phillips / N Amy Yewdall / Mark B Hampton / Juliet A Gerrard / Alok K Mitra /
Abstract: Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2- ...Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2-Cys Prxs are homodimers, which can self-associate to form complex assemblies that are hypothesized to have signaling and chaperone activity. Mitochondrial Prx3 forms dodecameric toroids, which can further stack to form filaments, the so-called high-molecular-weight (HMW) form that has putative holdase activity. We used single-particle analysis and helical processing of electron cryomicroscopy images of human Prx3 filaments induced by low pH to generate a ∼7-Å resolution 3D structure of the HMW form, the first such structure for a 2-Cys Prx. The pseudo-atomic model reveals interactions that promote the stacking of the toroids and shows that unlike previously reported data, the structure can accommodate a partially folded C terminus. The HMW filament lumen displays hydrophobic patches, which we hypothesize bestow holdase activity.
History
DepositionMar 19, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseAug 26, 2015-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6309.gif

Downloads & links

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Map

FileDownload / File: emd_6309.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human peroxiredoxin-3 filament
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.11567533 - 2.49763346
Average (Standard dev.)0.11275409 (±0.48321289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 241.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z241.920241.920241.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1.1162.4980.113

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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 (E. coli) / Recombinant strain: Rosetta (DE3) / Recombinant plasmid: pET151
SequenceUniProtKB: Thioredoxin-dependent peroxide reductase, mitochondrial

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 4 / Details: 20 mM HEPES, 75 mM NaCl
GridDetails: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 3 seconds blotting time

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateOct 1, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 45 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFTILT
Final reconstructionApplied symmetry - Helical parameters - Δz: 42.82 Å
Applied symmetry - Helical parameters - Δ&Phi: 8.06 °
Applied symmetry - Helical parameters - Axial symmetry: D6 (2x6 fold dihedral)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: OTHER / Software - Name: BSOFT, EMAN2, SPRING / Number images used: 466320

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