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- EMDB-13364: UVC treated Human apoferritin -

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Basic information

Entry
Database: EMDB / ID: EMD-13364
TitleUVC treated Human apoferritin
Map data
Sample
  • Complex: UVC treated Human apo Ferritin
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: CHLORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: water
Function / homology
Function and homology information


iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / 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: 2.1 Å
AuthorsRenault L / Depelteau JS / Briegel A
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)737.016.004European Union
European Union (EU)731005European Union
CitationJournal: Commun Biol / Year: 2022
Title: UVC inactivation of pathogenic samples suitable for cryo-EM analysis.
Authors: Jamie S Depelteau / Ludovic Renault / Nynke Althof / C Keith Cassidy / Luiza M Mendonça / Grant J Jensen / Guenter P Resch / Ariane Briegel /
Abstract: Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights ...Cryo-electron microscopy has become an essential tool to understand structure and function of biological samples. Especially for pathogens, such as disease-causing bacteria and viruses, insights gained by cryo-EM can aid in developing cures. However, due to the biosafety restrictions of pathogens, samples are often treated by chemical fixation to render the pathogen inert, affecting the ultrastructure of the sample. Alternatively, researchers use in vitro or ex vivo models, which are non-pathogenic but lack the complexity of the pathogen of interest. Here we show that ultraviolet-C (UVC) radiation applied at cryogenic temperatures can be used to eliminate or dramatically reduce the infectivity of Vibrio cholerae and the bacterial virus, the ICP1 bacteriophage. We show no discernable structural impact of this treatment of either sample using two cryo-EM methods: cryo-electron tomography followed by sub-tomogram averaging, and single particle analysis (SPA). Additionally, we applied the UVC irradiation to the protein apoferritin (ApoF), which is a widely used test sample for high-resolution SPA studies. The UVC-treated ApoF sample resulted in a 2.1 Å structure indistinguishable from an untreated published map. This research demonstrates that UVC treatment is an effective and inexpensive addition to the cryo-EM sample preparation toolbox.
History
DepositionAug 11, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJan 26, 2022-
Current statusJan 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pf1
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pf1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13364.png

Downloads & links

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Map

FileDownload / File: emd_13364.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 340 pix.
= 223.04 Å		0.66 Å/pix.
x 340 pix.
= 223.04 Å		0.66 Å/pix.
x 340 pix.
= 223.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.0125
Minimum - Maximum-0.021796891 - 0.04439689
Average (Standard dev.)0.000120030454 (±0.0021152517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 223.04001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6560.6560.656
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z223.040223.040223.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0220.0440.000

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Supplemental data

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Sample components

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Entire : UVC treated Human apo Ferritin

EntireName: UVC treated Human apo Ferritin
Components
  • Complex: UVC treated Human apo Ferritin
    • Protein or peptide: Ferritin heavy chain, N-terminally processed
  • Ligand: CHLORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: UVC treated Human apo Ferritin

SupramoleculeName: UVC treated Human apo Ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Ferritin heavy chain, N-terminally processed

MacromoleculeName: Ferritin heavy chain, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.274703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ASTSQVRQNY HQDSEAAINR QINLELYASY VYLSMSYYFD RDDVALKNFA KYFLHQSHEE REHAEKLMKL QNQRGGRIFL QDIKKPDCD DWESGLNAME CALHLEKNVN QSLLELHKLA TDKNDPHLCD FIETHYLNEQ VKAIKELGDH VTNLRKMGAP E SGLAEYLF DKHTLG

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 96 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 167 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 7207 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium Chloride
25.0 nMHEPESHEPES
1.0 mMDTT1,4-Dithiothreitol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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

Particle selectionNumber selected: 251350
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26735
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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