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- EMDB-13738: Horse spleen apoferritin -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-13738
TitleHorse spleen apoferritin
Map datahorse spleen apo-ferritin
Sample
  • Complex: apoferritin
  • Protein or peptide: Apoferritin (equine spleen)
Keywordsiron binding / iron release / iron regulation / METAL TRANSPORT
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsKoning RI / Renault L
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Not funded Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection.
Authors: Roman I Koning / Hildo Vader / Martijn van Nugteren / Peter A Grocutt / Wen Yang / Ludovic L R Renault / Abraham J Koster / Arnold C F Kamp / Michael Schwertner /
Abstract: The speed and efficiency of data collection and image processing in cryo-electron microscopy have increased over the last decade. However, cryo specimen preparation techniques have lagged and faster, ...The speed and efficiency of data collection and image processing in cryo-electron microscopy have increased over the last decade. However, cryo specimen preparation techniques have lagged and faster, more reproducible specimen preparation devices are needed. Here, we present a vitrification device with highly automated sample handling, requiring only limited user interaction. Moreover, the device allows inspection of thin films using light microscopy, since the excess liquid is removed through suction by tubes, not blotting paper. In combination with dew-point control, this enables thin film preparation in a controlled and reproducible manner. The advantage is that the quality of the prepared cryo specimen is characterized before electron microscopy data acquisition. The practicality and performance of the device are illustrated with experimental results obtained by vitrification of protein suspensions, lipid vesicles, bacterial and human cells, followed by imaged using single particle analysis, cryo-electron tomography, and cryo correlated light and electron microscopy.
History
DepositionOct 13, 2021-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13738.png

Downloads & links

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Map

FileDownload / File: emd_13738.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhorse spleen apo-ferritin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.048751656 - 0.100325
Average (Standard dev.)0.0002564622 (±0.0047383956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : apoferritin

EntireName: apoferritin
Components
  • Complex: apoferritin
  • Protein or peptide: Apoferritin (equine spleen)

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Supramolecule #1: apoferritin

SupramoleculeName: apoferritin / type: complex / ID: 1 / Parent: 0 / Details: Horse spleen apoferritin
Source (natural)Organism: Equus caballus (horse) / Organ: Spleen
Molecular weightTheoretical: 504 MDa

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Macromolecule #1: Apoferritin (equine spleen)

MacromoleculeName: Apoferritin (equine spleen) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
SSQIRQNYST EVEAAVNRLV NLYLRASYTY LSLGFYFDRD DVALEGVCHF FRELAEEKRE GAERLLKMQN QRGGRALFQD LQKPSQDEWG TTLDAMKAAI VLEKSLNQAL LDLHALGSAQ ADPHLCDFLE SHFLDEEVKL IKKMGDHLTN IQRLVGSQAG LGEYLFERLT LKHD

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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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.018000000000000002 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 294 K / Instrument: HOMEMADE PLUNGER
Details: Prototype of Linkam Plunger Sample applied by dipping grid in dispersion and excess solution removed by suction..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3348 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 689633
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 91000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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