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- EMDB-32695: High resolution of apo-ferritin embedded in crystalline ice -

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Basic information

Entry
Database: EMDB / ID: EMD-32695
TitleHigh resolution of apo-ferritin embedded in crystalline ice
Map dataEM map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera.
Sample
  • Complex: Human apo-ferritin
Keywordscomplex / Transport Protein
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 uptake and transport / ferrous iron binding / iron ion transport / 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 / cytosol / cytoplasm
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: 1.76 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: Shi H / Wu C / Zhang X
History
DepositionJan 24, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_32695.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of Human apo-ferritin embedded in crystal datasets frozen at -183 degree collected via Titan Krios by K2 camera.
Voxel sizeX=Y=Z: 0.52 Å
Density
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.07623926 - 0.14414173
Average (Standard dev.)0.000096651085 (±0.011997575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 156.0 Å
α=β=γ: 90.0 °

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Supplemental data

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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 / 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 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 / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94792
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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