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Open data
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Basic information
Entry | Database: PDB / ID: 8edu | |||||||||||||||
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Title | Mycobacteriophage Muddy capsid | |||||||||||||||
![]() | Capsid | |||||||||||||||
![]() | VIRUS / Bacteriophage / Mycobacteriophage / HK97-fold / Capsid | |||||||||||||||
Function / homology | Phage capsid / Phage capsid family / Capsid![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
![]() | Freeman, K.G. / White, S.J. / Huet, A. / Conway, J.F. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability. Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten ...Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten / Janne Ravantti / Simon J White / ![]() ![]() Abstract: Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. ...Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. After the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination of 10 capsids, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. We show that the actinobacteriophage major capsid proteins can be classified into 15 groups based upon their HK97-fold. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 678.9 KB | Display | ![]() |
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PDB format | ![]() | 575.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 84.4 KB | Display | |
Data in CIF | ![]() | 126.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28039MC ![]() 8e16C ![]() 8eb4C ![]() 8ec2C ![]() 8ec8C ![]() 8eciC ![]() 8ecjC ![]() 8eckC ![]() 8ecnC ![]() 8ecoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 34670.102 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mycobacterium phage Muddy / Type: VIRUS Details: Phage Muddy particles generated by amplification on bacterial host and purification via CsCl gradient. Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Mycolicibacterium smegmatis MC2 155 | |||||||||||||||||||||||||
Virus shell | Diameter: 710 nm / Triangulation number (T number): 7 | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1027 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Details: Standard CTF correction inside RELION's reconstruction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 28207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25244 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL Details: Amino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde. |