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- EMDB-14348: 64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms wi... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-14348
Title64K CDS Apoferritin map reconstructed from 32.5K sub-tomograms with emClarity
Map datasharpened emClarity map
Sample
  • Complex: human Apoferritin
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 2.7 Å
AuthorsClare DK
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Not fundedcm26464-2 United Kingdom
CitationJournal: To Be Published
Title: 2.7 A STRUCTURE OF HUMAN APOFERRITIN OBTAINED FROM TITAN KRIOS 2 AT eBIC, DLS UNDER COMMISSIONING SESSION CM26464-2 USING SUB-TOMOGRAM AVERAGING
Authors: Clare DK
History
DepositionFeb 14, 2022-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateFeb 22, 2023-
Current statusFeb 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14348.png

Downloads & links

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Map

FileDownload / File: emd_14348.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened emClarity map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 177 pix.
= 240.012 Å		1.36 Å/pix.
x 177 pix.
= 240.012 Å		1.36 Å/pix.
x 177 pix.
= 240.012 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.73
Minimum - Maximum-9.368363 - 17.010504
Average (Standard dev.)0.04741835 (±0.9513701)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions177177177
Spacing177177177
CellA=B=C: 240.012 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Relion sharpened emClarity/CisTEM map

Fileemd_14348_additional_1.map
AnnotationRelion sharpened emClarity/CisTEM 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 : human Apoferritin

EntireName: human Apoferritin
Components
  • Complex: human Apoferritin

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Supramolecule #1: human Apoferritin

SupramoleculeName: human Apoferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 / Details: Heavy chain
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM TCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time of 2.5 seconds.
DetailsThe apoferritin sample was applied to in-house graphene-coated Quantifoil r2/2 EM grid

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsDose symmetric tilt series
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.5 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 64000
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) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 32500
ExtractionNumber tomograms: 27 / Number images used: 32500 / Reference model: from SPA / Method: emClarity / Software - Name: emClarity / Details: Template matching
Final 3D classificationSoftware - Name: emClarity
Final angle assignmentType: PROJECTION MATCHING / Software - Name: emClarity
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7r5o

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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