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- EMDB-35981: Single-particle cryo-EM structure of mouse apoferritin at 1.49 An... -

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Basic information

Entry
Database: EMDB / ID: EMD-35981
TitleSingle-particle cryo-EM structure of mouse apoferritin at 1.49 Angstrom resolution (Dataset B)
Map dataPostprocess_masked
Sample
  • Complex: Apoferritin
    • Protein or peptide: Ferritin heavy chain
Keywordssingle-particle cryo-EM / Cold field emission / CFEG / Apoferritin / CRYO ARM / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.49 Å
AuthorsKawakami K / Maki-Yonekura S / Hamaguchi T / Takaba K / Yonekura K
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JPMJMI20G5 Japan
Japan Society for the Promotion of Science (JSPS)JPMJCR18J2 Japan
CitationJournal: Commun Chem / Year: 2023
Title: Measurement of charges and chemical bonding in a cryo-EM structure.
Authors: Saori Maki-Yonekura / Keisuke Kawakami / Kiyofumi Takaba / Tasuku Hamaguchi / Koji Yonekura /
Abstract: Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, ...Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.
History
DepositionApr 21, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35981.png

Downloads & links

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Map

FileDownload / File: emd_35981.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocess_masked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 600 pix.
= 297. Å		0.5 Å/pix.
x 600 pix.
= 297. Å		0.5 Å/pix.
x 600 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.495 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0285
Minimum - Maximum-0.119928986 - 0.3337094
Average (Standard dev.)0.000025903468 (±0.0045806053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half1 map

Fileemd_35981_half_map_1.map
AnnotationHalf1_map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2 map

Fileemd_35981_half_map_2.map
AnnotationHalf2_map
Projections & Slices
AxesZYX

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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: Ferritin heavy chain

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Supramolecule #1: Apoferritin

SupramoleculeName: Apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Mus musculus (house mouse)
SequenceString:
PSQVRQNYHQ DAEAAINRQI NLELYASYVY LSMSCYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDRDDWE SGLNAMECAL HLEKSVNQSL LELHKLATDK NDPHLCDFIE TYYLSEQVKS IKELGDHVTN LRKMGAPEAG MAEYLFDKHT LG

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 311583
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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