+Open data
-Basic information
Entry | Database: PDB / ID: 5vly | |||||||||||||||
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Title | Asymmetric unit for the coat proteins of phage Qbeta | |||||||||||||||
Components | Capsid protein | |||||||||||||||
Keywords | VIRUS / Qbeta / ssRNA / phage | |||||||||||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / translation repressor activity / structural molecule activity / RNA binding Similarity search - Function | |||||||||||||||
Biological species | Escherichia phage Qbeta (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Cui, Z. / Zhang, J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis. Authors: Zhicheng Cui / Karl V Gorzelnik / Jeng-Yih Chang / Carrie Langlais / Joanita Jakana / Ry Young / Junjie Zhang / Abstract: In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the ...In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Qβ the maturation protein, A, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A binding were found to be due to the intimate fit between A and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures. | |||||||||||||||
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 | 5vly.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vly.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vly_validation.pdf.gz | 911.5 KB | Display | wwPDB validaton report |
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Full document | 5vly_full_validation.pdf.gz | 913.1 KB | Display | |
Data in XML | 5vly_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 5vly_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/5vly ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vly | HTTPS FTP |
-Related structure data
Related structure data | 8708MC 8707C 8709C 8710C 8711C 5vlzC 5vm7C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 14268.071 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: P03615 |
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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 |
-Sample preparation
Component | Name: Enterobacteria phage Qbeta / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Enterobacteria phage Qbeta (virus) |
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 |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: Blotted for 6s, Plunged into liquid ethane (FEI VITROBOT MARK III) |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 30000 X |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 171602 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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