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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex | ||||||||||||
![]() | unsharpened, filtered to FSC0.143 resolution cutoff | ||||||||||||
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![]() | bacteriophage / capsid / structural virion protein / VIRAL PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 19.0 Å | ||||||||||||
![]() | Laughlin TG / Villa E | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 21.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.9 KB 19.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.6 KB | Display | ![]() |
Images | ![]() | 183.5 KB | ||
Masks | ![]() | 23.8 MB | ![]() | |
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() ![]() | 46.9 MB 18.1 MB 18.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 924.5 KB | Display | ![]() |
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Full document | ![]() | 924.1 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | unsharpened, filtered to FSC0.143 resolution cutoff | ||||||||||||||||||||
Voxel size | X=Y=Z: 8 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Composite virion map consisting of: Capsid vertex, collar,...
File | emd_28003_additional_1.map | ||||||||||||
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Annotation | Composite virion map consisting of: Capsid vertex, collar, tail sheath, and baseplate maps. | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_28003_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28003_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex
Entire | Name: Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex |
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Components |
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-Supramolecule #1: Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex
Supramolecule | Name: Erwinia phage vB_EamM_RAY (RAY) Capsid Vertex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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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 current, PELCO EasiGlo |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
Details | cell suspension |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |