+Open data
-Basic information
Entry | Database: PDB / ID: 5muu | ||||||
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Title | dsRNA bacteriophage phi6 nucleocapsid | ||||||
Components |
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Keywords | VIRUS / icosahedral virus capsid shell | ||||||
Function / homology | Function and homology information T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral procapsid / viral genome packaging / viral inner capsid / viral outer capsid / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / viral capsid / viral nucleocapsid ...T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral procapsid / viral genome packaging / viral inner capsid / viral outer capsid / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / viral capsid / viral nucleocapsid / RNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas phage phi6 (bacteriophage) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Sun, Z. / El Omari, K. / Sun, X. / Ilca, S.L. / Kotecha, A. / Stuart, D.I. / Poranen, M.M. / Huiskonen, J.T. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Authors: Zhaoyang Sun / Kamel El Omari / Xiaoyu Sun / Serban L Ilca / Abhay Kotecha / David I Stuart / Minna M Poranen / Juha T Huiskonen / Abstract: Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by ...Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5muu.cif.gz | 550.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5muu.ent.gz | 459 KB | Display | PDB format |
PDBx/mmJSON format | 5muu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Data in XML | 5muu_validation.xml.gz | 645 B | Display | |
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Data in CIF | 5muu_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5muu ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5muu | HTTPS FTP |
-Related structure data
Related structure data | 3571MC 3572C 3573C 5muvC 5muwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 85080.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage) / References: UniProt: P11126 #2: Protein | | Mass: 35198.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage) References: UniProt: P11125, nucleoside-triphosphate phosphatase #3: Protein | Mass: 16018.418 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage) / References: UniProt: P07579 |
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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 |
Crystal symmetry | ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name H-M: P1 |
-Sample preparation
Component | Name: Pseudomonas phage phi6 / Type: VIRUS Details: The viral envelope was removed by Triton X-114 extraction Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Pseudomonas phage phi6 (bacteriophage) | |||||||||||||||
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION | |||||||||||||||
Natural host | Organism: Pseudomonas syringae / Strain: pv.phaseolicola HB10Y | |||||||||||||||
Virus shell |
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Buffer solution | pH: 7.2 | |||||||||||||||
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 300 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 120 K / Temperature (min): 80 K |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 0.73 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 900 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3710 / Movie frames/image: 22 / Used frames/image: 1-22 |
-Processing
Software | Name: PHENIX / Version: dev_2044: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Crystal symmetry | ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name H-M: P1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 16466 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13291 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building |
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Refine LS restraints |
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