|Entry||Database: EMDB / ID: EMD-0618|
|Title||Icosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid|
|Sample||Thermus phage P7426 (bacteriophage):|
virus / Major head protein / P74-26 Head Decoration Protein
|Function / homology||Major capsid protein GpE / Phage major capsid protein E / Uncharacterized protein / Major head protein|
Function and homology information
|Biological species||Thermus phage P7426 (bacteriophage) / Thermus virus P74-26 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / Resolution: 2.8 Å|
|Authors||Stone NP / Demo G / Agnello E / Kelch BA|
|Funding support|| United States, 1 items |
|Citation||Journal: Nat Commun / Year: 2019|
Title: Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure.
Authors: Nicholas P Stone / Gabriel Demo / Emily Agnello / Brian A Kelch /
Abstract: The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To ...The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.
|Validation Report||PDB-ID: 6o3h|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0618.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.059 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Thermus phage P7426
|Entire||Name: Thermus phage P7426 (bacteriophage) / Number of components: 3|
-Component #1: virus, Thermus phage P7426
|Virus||Name: Thermus phage P7426 / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER|
|Species||Species: Thermus phage P7426 (bacteriophage)|
|Source (natural)||Host Species: Thermus thermophilus (bacteria) / Host species strain: HB8|
|Shell #1||Name of element: P74-26 capsid / Diameter: 824.0 Å / T number (triangulation number): 7|
-Component #2: protein, Major head protein
|Protein||Name: Major head protein / Number of Copies: 7 / Recombinant expression: No|
|Mass||Theoretical: 46.680754 kDa|
|Source||Species: Thermus virus P74-26 (bacteriophage)|
-Component #3: protein, P74-26 Head Decoration Protein
|Protein||Name: P74-26 Head Decoration Protein / Number of Copies: 7 / Recombinant expression: No|
|Mass||Theoretical: 16.37663 kDa|
|Source||Species: Thermus virus P74-26 (bacteriophage)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Support film||45 second glow discharge, negative polarity, 20 mA|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 200.0 - 1200.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 4611|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 23174|
|3D reconstruction||Software: FREALIGN / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Target criteria: Correlation Coefficient / Refinement space: REAL|
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