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- EMDB-32703: apo-ferritin embedded in crystalline ice frozen at -183 degree -

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Basic information

Entry
Database: EMDB / ID: EMD-32703
Titleapo-ferritin embedded in crystalline ice frozen at -183 degree
Map dataApo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera
Sample
  • Complex: Human apo-ferritin
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 / Resolution: 2.4 Å
AuthorsZhang X / Shi H / Wu C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Structure / Year: 2023
Title: Addressing compressive deformation of proteins embedded in crystalline ice.
Authors: Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. ...For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
History
DepositionJan 25, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32703.png

Downloads & links

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Map

FileDownload / File: emd_32703.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 300 pix.
= 150. Å		0.5 Å/pix.
x 300 pix.
= 150. Å		0.5 Å/pix.
x 300 pix.
= 150. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0189
Minimum - Maximum-0.02204997 - 0.04494718
Average (Standard dev.)0.00021066182 (±0.005102958)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 150.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32703_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: Apo-ferritin map from standard freezing datasets collected via...

Fileemd_32703_additional_1.map
AnnotationApo-ferritin map from standard freezing datasets collected via FEI Arctica by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -140...

Fileemd_32703_additional_2.map
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -140 degree collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Apo-ferritin map from standard freezing datasets collected via...

Fileemd_32703_additional_3.map
AnnotationApo-ferritin map from standard freezing datasets collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -60...

Fileemd_32703_additional_4.map
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -60 degree collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Apo-ferritin map from crystal-embedded datasets frozen at -100...

Fileemd_32703_additional_5.map
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -100 degree collected via Titan Krios by K2 camera
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apo-ferritin map from crystal-embedded datasets frozen at -183...

Fileemd_32703_half_map_1.map
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera. The half map of apo-ferritin was flipped and centered.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Apo-ferritin map from crystal-embedded datasets frozen at -183...

Fileemd_32703_half_map_2.map
AnnotationApo-ferritin map from crystal-embedded datasets frozen at -183 degree collected via FEI Arctica by K2 camera. The half map of apo-ferritin was flipped and centered.
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 apo-ferritin

EntireName: Human apo-ferritin
Components
  • Complex: Human apo-ferritin

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Supramolecule #1: Human apo-ferritin

SupramoleculeName: Human apo-ferritin / type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 440 KDa

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Sugar embeddingMaterial: crystalline ice

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9200
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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