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- EMDB-3233: Volta phase plate cryo-EM of the small protein complex Prx3 -

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Basic information

Entry
Database: EMDB / ID: EMD-3233
TitleVolta phase plate cryo-EM of the small protein complex Prx3
Map dataVolta phase plate reconstruction of hPrx3
Sample
  • Sample: Human peroxiredoxin 3
  • Protein or peptide: Peroxiredoxin 3
KeywordsPeroxidase / antioxidant
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
: / 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: 4.4 Å
AuthorsKhoshouei M / Radjainia M / Phillips AJ / Gerrard JA / Mitra AK / Plitzko JM / Baumeister W / Danev R
CitationJournal: Nat Commun / Year: 2016
Title: Volta phase plate cryo-EM of the small protein complex Prx3.
Authors: Maryam Khoshouei / Mazdak Radjainia / Amy J Phillips / Juliet A Gerrard / Alok K Mitra / Jürgen M Plitzko / Wolfgang Baumeister / Radostin Danev /
Abstract: Cryo-EM of large, macromolecular assemblies has seen a significant increase in the numbers of high-resolution structures since the arrival of direct electron detectors. However, sub-nanometre ...Cryo-EM of large, macromolecular assemblies has seen a significant increase in the numbers of high-resolution structures since the arrival of direct electron detectors. However, sub-nanometre resolution cryo-EM structures are rare compared with crystal structure depositions, particularly for relatively small particles (<400 kDa). Here we demonstrate the benefits of Volta phase plates for single-particle analysis by time-efficient cryo-EM structure determination of 257 kDa human peroxiredoxin-3 dodecamers at 4.4 Å resolution. The Volta phase plate improves the applicability of cryo-EM for small molecules and accelerates structure determination.
History
DepositionNov 6, 2015-
Header (metadata) releaseJan 13, 2016-
Map releaseFeb 3, 2016-
UpdateFeb 10, 2016-
Current statusFeb 10, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0368
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0368
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3233.tif

Downloads & links

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Map

FileDownload / File: emd_3233.map.gz / Format: CCP4 / Size: 13.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolta phase plate reconstruction of hPrx3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 152 pix.
= 264.48 Å		1.74 Å/pix.
x 152 pix.
= 264.48 Å		1.74 Å/pix.
x 152 pix.
= 264.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0368 / Movie #1: 0.0368
Minimum - Maximum-0.04875568 - 0.1705908
Average (Standard dev.)0.00093987 (±0.0076915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions152152152
Spacing152152152
CellA=B=C: 264.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z152152152
origin x/y/z0.0000.0000.000
length x/y/z264.480264.480264.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS152152152
D min/max/mean-0.0490.1710.001

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Supplemental data

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Sample components

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Entire : Human peroxiredoxin 3

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

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Supramolecule #1000: Human peroxiredoxin 3

SupramoleculeName: Human peroxiredoxin 3 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Dodecamer / Number unique components: 1
Molecular weightTheoretical: 257 KDa

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Macromolecule #1: Peroxiredoxin 3

MacromoleculeName: Peroxiredoxin 3 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Mitochondria / Location in cell: Matrix
Molecular weightTheoretical: 257 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET
SequenceUniProtKB: Thioredoxin-dependent peroxide reductase, mitochondrial

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 150mM NaCl, 20mM Hepes
GridDetails: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 85 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK III / Method: Blotting time: 4seconds

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: Quantum post-column energy filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsVolta Phase Plate
DateJul 1, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 28700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 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

Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 8000
FSC plot (resolution estimation)

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