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- EMDB-31736: Structure of Apoferritin -

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Basic information

Entry
Database: EMDB / ID: EMD-31736
TitleStructure of Apoferritin
Map datathe reconstruction of full frame
Sample
  • Complex: Human apoferritin
    • Protein or peptide: Ferritin heavy chain
Keywordscomplex / TRANSPORT PROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / Scavenging by Class A Receptors / negative regulation of ferroptosis / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / iron ion transport / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / ficolin-1-rich granule lumen / intracellular iron ion homeostasis / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Ferritin heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.89 Å
AuthorsZhang X / Wu C / Shi H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: QRB Discov / Year: 2021
Title: Low-cooling-rate freezing in biomolecular cryo-electron microscopy for recovery of initial frames.
Authors: Chunling Wu / Huigang Shi / Dongjie Zhu / Kelong Fan / Xinzheng Zhang /
Abstract: When biological samples are first exposed to electrons in cryo-electron microcopy (cryo-EM), proteins exhibit a rapid 'burst' phase of beam-induced motion that cannot be corrected with software. This ...When biological samples are first exposed to electrons in cryo-electron microcopy (cryo-EM), proteins exhibit a rapid 'burst' phase of beam-induced motion that cannot be corrected with software. This lowers the quality of the initial frames, which are the least damaged by the electrons. Hence, they are commonly excluded or down-weighted during data processing, reducing the undamaged signal and the resolution in the reconstruction. By decreasing the cooling rate during sample preparation, either with a cooling-rate gradient or by increasing the freezing temperature, we show that the quality of the initial frames for various protein and virus samples can be recovered. Incorporation of the initial frames in the reconstruction increases the resolution by an amount equivalent to using ~60% more data. Moreover, these frames preserve the high-quality cryo-EM densities of radiation-sensitive residues, which is often damaged or very weak in canonical three-dimensional reconstruction. The improved freezing conditions can be easily achieved using existing devices and enhance the overall quality of cryo-EM structures.
History
DepositionAug 19, 2021-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31736.png

Downloads & links

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Map

FileDownload / File: emd_31736.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe reconstruction of full frame
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 400 pix.
= 206. Å		0.52 Å/pix.
x 400 pix.
= 206. Å		0.52 Å/pix.
x 400 pix.
= 206. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.515 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.052408278 - 0.09492372
Average (Standard dev.)-0.00014215909 (±0.0053789644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: the eighth frame of per-frame reconstruction

Fileemd_31736_additional_1.map
Annotationthe eighth frame of per-frame reconstruction
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Additional map: the tenth frame of per-frame reconstruction

Fileemd_31736_additional_10.map
Annotationthe tenth frame of per-frame reconstruction
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Additional map: the seventh frame of per-frame reconstruction

Fileemd_31736_additional_2.map
Annotationthe seventh frame of per-frame reconstruction
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Additional map: the second frame of per-frame reconstruction

Fileemd_31736_additional_3.map
Annotationthe second frame of per-frame reconstruction
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Additional map: the first frame of per-frame reconstruction

Fileemd_31736_additional_4.map
Annotationthe first frame of per-frame reconstruction
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Additional map: the third frame of per-frame reconstruction

Fileemd_31736_additional_5.map
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Additional map: the fifth frame of per-frame reconstruction

Fileemd_31736_additional_6.map
Annotationthe fifth frame of per-frame reconstruction
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Additional map: the fourth frame of per-frame reconstruction

Fileemd_31736_additional_7.map
Annotationthe fourth frame of per-frame reconstruction
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Additional map: the sixth frame of per-frame reconstruction

Fileemd_31736_additional_8.map
Annotationthe sixth frame of per-frame reconstruction
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Additional map: the ninth frame of per-frame reconstruction

Fileemd_31736_additional_9.map
Annotationthe ninth frame of per-frame reconstruction
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Sample components

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Entire : Human apoferritin

EntireName: Human apoferritin
Components
  • Complex: Human apoferritin
    • Protein or peptide: Ferritin heavy chain

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Supramolecule #1: Human apoferritin

SupramoleculeName: Human apoferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 440 KDa

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Macromolecule #1: Ferritin heavy chain

MacromoleculeName: Ferritin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.116547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TSQVRQNYHQ DSEAAINRQI NLELYASYVY LSMSYYFDRD DVALKNFAKY FLHQSHEERE HAEKLMKLQN QRGGRIFLQD IKKPDCDDW ESGLNAMECA LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT NLRKMGAPES G LAEYLFDK HTLG

UniProtKB: Ferritin heavy chain

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296695
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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