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- EMDB-13403: Cryo-EM map of WT ICP1 bacteriophage capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-13403
TitleCryo-EM map of WT ICP1 bacteriophage capsid
Map dataCryo-EM map of WT ICP1 bacteriophage capsid
Sample
  • Virus: Vibrio phage ICP1 (virus)
Biological speciesVibrio phage ICP1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsDepelteau JS / Briegel A
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)737.016.004European Union
Netherlands Organisation for Scientific Research (NWO)84.034.014European 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 16, 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: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13403.png

Downloads & links

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Map

FileDownload / File: emd_13403.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of WT ICP1 bacteriophage capsid
Voxel sizeX=Y=Z: 1.63696 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.0013168743 - 0.03886032
Average (Standard dev.)0.0011981607 (±0.0039276658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 1227.7178 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.63695733333331.63695733333331.6369573333333
M x/y/z750750750
origin x/y/z0.0000.0000.000
length x/y/z1227.7181227.7181227.718
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS750750750
D min/max/mean-0.0010.0390.001

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Supplemental data

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Sample components

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Entire : Vibrio phage ICP1

EntireName: Vibrio phage ICP1 (virus)
Components
  • Virus: Vibrio phage ICP1 (virus)

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Supramolecule #1: Vibrio phage ICP1

SupramoleculeName: Vibrio phage ICP1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 979525 / Sci species name: Vibrio phage ICP1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vibrio cholerae (bacteria) / Strain: N16961

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 34.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4096
FSC plot (resolution estimation)

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