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- EMDB-33707: Apoferritin structure at 1.46 angstrom resolution by CryoARM300 e... -

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Basic information

Entry
Database: EMDB / ID: EMD-33707
TitleApoferritin structure at 1.46 angstrom resolution by CryoARM300 equipped with Apollo
Map data
Sample
  • Complex: Apoferritin
    • Protein or peptide: Apoferritin
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.47 Å
AuthorsBammes B / Spilman M / Sakamoto M / Fukumura T / Konyuba Y / Okunishi E
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Apoferritin structure at 1.46 angstrom resolution by CryoARM300 equipped with Apollo
Authors: Bammes B / Spilman M / Sakamoto M / Fukumura T / Konyuba Y / Okunishi E
History
DepositionJun 27, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33707.png

Downloads & links

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Map

FileDownload / File: emd_33707.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 288 pix.
= 200.88 Å		0.7 Å/pix.
x 288 pix.
= 200.88 Å		0.7 Å/pix.
x 288 pix.
= 200.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0462
Minimum - Maximum-0.19332832 - 0.46937612
Average (Standard dev.)0.00032839997 (±0.01352399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 200.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33707_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33707_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_33707_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 : Apoferritin

EntireName: Apoferritin
Components
  • Complex: Apoferritin
    • Protein or peptide: Apoferritin

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Apoferritin

MacromoleculeName: Apoferritin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTASPSQVR QNYHQDAEAA INRQINLELY ASYVYLSMSC YFDRDDVALK NFAKYFLHQS HEEREHAEKL MKLQNQRGGR IFLQDIKKPD RDDWESGLNA MECALHLEKS VNQSLLELHK LATDKNDPHL CDFIETYYLS EQVKSIKELG DHVTNLRKMG APEAGMAEYL FDKHTLGHGD ES

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESN-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: OTHER / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsApollo
Particle selectionNumber selected: 1412541
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 821926
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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