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- EMDB-10012: Apoferritin map obtained from grids prepared with the Preassis method -

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Basic information

Entry
Database: EMDB / ID: EMD-10012
TitleApoferritin map obtained from grids prepared with the Preassis method
Map dataApoferritin map Preassis, sharpened masked
Sample
  • Complex: Apoferritin
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsZhao J / Xu H / Carroni M / Zou X
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: A simple pressure-assisted method for cryo-EM specimen preparation
Authors: Zhao J / Xu H / Carroni M / Lebrette H / Wallden K / Moe A / Matsuoka R / Hogbom M / Zou X
History
DepositionJun 1, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0318
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10012.png

Downloads & links

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Map

FileDownload / File: emd_10012.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoferritin map Preassis, sharpened masked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0318 / Movie #1: 0.0318
Minimum - Maximum-0.07269093 - 0.13964175
Average (Standard dev.)0.00027894627 (±0.0049757683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.000318.000318.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0730.1400.000

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Supplemental data

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Additional map: Apoferritin map Preassis, sharpened

Fileemd_10012_additional.map
AnnotationApoferritin map Preassis, sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apoferritin map Preassis, unsharpened halfmap2

Fileemd_10012_half_map_1.map
AnnotationApoferritin map Preassis, unsharpened halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apoferritin map Preassis, unsharpened halfmap1

Fileemd_10012_half_map_2.map
AnnotationApoferritin map Preassis, unsharpened halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apoferritin

EntireName: Apoferritin
Components
  • Complex: Apoferritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Equus caballus (horse)
Recombinant expressionOrganism: Escherichia coli #1/H766 (bacteria)

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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

Concentration0.18 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-Cl, pH 7.5; 150 mM NaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Details: New pressure assisted method, Preassis.
DetailsHorse spleen apoferritin was bought from Sigma (A3641, 481.2 kDa). The original concentration was about 35 mg/ml. A buffer (20 mM Tris-Cl, pH 7.5; 150 mM NaCl) was filtered with a 0.2 um filter. The final concentraion used was 0.18mg/mL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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: EMDB MAP
EMDB ID:

3854


Details: The staring map was filtered to 60A and used to get the first right orientation on the symmetry axis
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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