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- EMDB-16032: Structure of mouse heavy chain apoferritin solved by subtomogram ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16032
TitleStructure of mouse heavy chain apoferritin solved by subtomogram averaging of 100 tilt series in Warp/M
Map data
Sample
  • Complex: Ferritin heavy chain
KeywordsApoferritin / Subtomogram averaging / STA / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 1.6 Å
AuthorsObr M / Yang W / Karia D / Koh FA / Kotecha A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of mouse heavy chain apoferritin solved by subtomogram averaging of 10 tilt series in Warp/M
Authors: Obr M / Yang W / Karia D / Koh FA / Kotecha A
History
DepositionOct 27, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16032.png

Downloads & links

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Map

FileDownload / File: emd_16032.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0024
Minimum - Maximum-0.0051480355 - 0.015527511
Average (Standard dev.)0.0000015679577 (±0.00030579776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16032_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ferritin heavy chain

EntireName: Ferritin heavy chain
Components
  • Complex: Ferritin heavy chain

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Supramolecule #1: Ferritin heavy chain

SupramoleculeName: Ferritin heavy chain / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
DetailsTilt series acquired with Hagen scheme +-48 degrees with 3 increment
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 0.5 sec. / Average electron dose: 3.5 e/Å2 / Details: Imaged with TFS Selectris X and Falcon 4i
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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
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

Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. nb20201104) / Software - details: M / Number subtomograms used: 31478
ExtractionNumber tomograms: 100 / Number images used: 31478 / Method: Automatic 2D picking / Software: (Name: RELION (ver. 4), Warp (ver. nb20201104))
Details: Particles picked in 2D using the 0 degrees tilt image. Z coordinate was determined using ice layer fitting.
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Warp (ver. nb20201104) / Software - details: M
FSC plot (resolution estimation)

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