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Open data
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Basic information
Entry | Database: PDB / ID: 7lhd | |||||||||||||||
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Title | The complete model of phage Qbeta virion | |||||||||||||||
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![]() | VIRUS/RNA / Bacteriophage / Virus / Virion / VIRUS-RNA complex | |||||||||||||||
Function / homology | ![]() suppression by virus of host cell wall biogenesis / suppression by virus of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / T=3 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / translation repressor activity / viral release from host cell by cytolysis / virion component / structural molecule activity / RNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||
![]() | Chang, J.Y. / Zhang, J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles. Authors: Jeng-Yih Chang / Karl V Gorzelnik / Jirapat Thongchol / Junjie Zhang / ![]() Abstract: The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) ...The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical = 3 icosahedral, larger = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.7 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 859.8 KB | Display | |
Data in CIF | ![]() | 1.3 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 23336MC ![]() 7lgeC ![]() 7lgfC ![]() 7lggC ![]() 7lghC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: RNA chain | Mass: 1352016.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 48613.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 14268.071 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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: Escherichia virus Qbeta / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company | |||||||||||||||||||||
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EM imaging |
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Image recording |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86081 / Symmetry type: POINT |