+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13364 | |||||||||
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Title | UVC treated Human apoferritin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ferritin / METAL BINDING PROTEIN | |||||||||
Function / homology | Function and homology information iron ion sequestering activity / : / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / : / negative regulation of ferroptosis / 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 / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Renault L / Depelteau JS | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13364.map.gz | 20 MB | EMDB map data format | |
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Header (meta data) | emd-13364-v30.xml emd-13364.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13364_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_13364.png | 207.7 KB | ||
Filedesc metadata | emd-13364.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13364 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13364 | HTTPS FTP |
-Validation report
Summary document | emd_13364_validation.pdf.gz | 409.2 KB | Display | EMDB validaton report |
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Full document | emd_13364_full_validation.pdf.gz | 408.8 KB | Display | |
Data in XML | emd_13364_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_13364_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13364 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13364 | HTTPS FTP |
-Related structure data
Related structure data | 7pf1MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13364.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.656 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : UVC treated Human apo Ferritin
Entire | Name: UVC treated Human apo Ferritin |
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Components |
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-Supramolecule #1: UVC treated Human apo Ferritin
Supramolecule | Name: UVC treated Human apo Ferritin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: Ferritin heavy chain, N-terminally processed
Macromolecule | Name: Ferritin heavy chain, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.274703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ASTSQVRQNY HQDSEAAINR QINLELYASY VYLSMSYYFD RDDVALKNFA KYFLHQSHEE REHAEKLMKL QNQRGGRIFL QDIKKPDCD DWESGLNAME CALHLEKNVN QSLLELHKLA TDKNDPHLCD FIETHYLNEQ VKAIKELGDH VTNLRKMGAP E SGLAEYLF DKHTLG UniProtKB: Ferritin heavy chain |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 96 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 167 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 7207 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |