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- EMDB-27973: Erwinia amylovora 70S Ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-27973
TitleErwinia amylovora 70S Ribosome
Map dataunsharpened, filtered to FSC0.143 cutoff
Sample
  • Complex: Erwinia amylovora 70S Ribosome
KeywordsRibosome
Biological speciesErwinia amylovora (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.9 Å
AuthorsLaughlin TG / Villa E
Funding support United States, 3 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129245 United States
National Science Foundation (NSF, United States)DBI 1920374 United States
CitationJournal: bioRxiv / Year: 2023
Title: Identifying the core genome of the nucleus-forming bacteriophage family and characterization of phage RAY.
Abstract: We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic ...We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
History
DepositionAug 28, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27973.png

Downloads & links

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Map

FileDownload / File: emd_27973.map.gz / Format: CCP4 / Size: 2.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened, filtered to FSC0.143 cutoff
Voxel sizeX=Y=Z: 4.265 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.24683961 - 0.88442236
Average (Standard dev.)0.010976705 (±0.1176279)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions888888
Spacing888888
CellA=B=C: 375.31998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27973_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27973_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27973_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Erwinia amylovora 70S Ribosome

EntireName: Erwinia amylovora 70S Ribosome
Components
  • Complex: Erwinia amylovora 70S Ribosome

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Supramolecule #1: Erwinia amylovora 70S Ribosome

SupramoleculeName: Erwinia amylovora 70S Ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Erwinia amylovora (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5 / Details: Lysogeny Broth containing 5% trehalose
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 19.0 kPa / Details: PELCO EasiGlo at 20 mA current
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Detailscell suspension

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000
Specialist opticsEnergy filter - Name: GIF Quantum LS / 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average electron dose: 2.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 26 / Number images used: 74713 / Reference model: ab initio reference / Method: template-matching / Software - Name: Warp
Final 3D classificationNumber classes: 5 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 55299
FSC plot (resolution estimation)

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