+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28008 | ||||||||||||
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Title | Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Bacteriophage / structural protein / viral tubulin / VIRAL PROTEIN | ||||||||||||
Biological species | Erwinia phage vB_EamM_RAY (virus) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.0 Å | ||||||||||||
Authors | Laughlin TG / Villa E | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28008.map.gz | 503.1 KB | EMDB map data format | |
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Header (meta data) | emd-28008-v30.xml emd-28008.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28008_fsc.xml | 2 KB | Display | FSC data file |
Images | emd_28008.png | 41.7 KB | ||
Masks | emd_28008_msk_1.map | 550.3 KB | Mask map | |
Filedesc metadata | emd-28008.cif.gz | 4.8 KB | ||
Others | emd_28008_half_map_1.map.gz emd_28008_half_map_2.map.gz | 404 KB 405.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28008 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28008.map.gz / Format: CCP4 / Size: 549.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 4.265 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28008_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28008_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28008_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament
Entire | Name: Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament |
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Components |
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-Supramolecule #1: Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament
Supramolecule | Name: Erwinia phage vB_EamM_RAY (RAY) Putative PhuZ Filament type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Erwinia phage vB_EamM_RAY (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 / Details: Lysogeny Broth containing 5% trehalose |
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Grid | Model: 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: 0.019 kPa / Details: 20 mA in PELCO EasiGLO |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
Details | cell suspension |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film 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 |