+Open data
-Basic information
Entry | Database: PDB / ID: 5hx2 | ||||||
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Title | In vitro assembled star-shaped hubless T4 baseplate | ||||||
Components |
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Keywords | VIRAL PROTEIN / T4 / baseplate / complex | ||||||
Function / homology | Function and homology information virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Yap, M.L. / Klose, T. / Fokine, A. / Rossmann, M.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Role of bacteriophage T4 baseplate in regulating assembly and infection. Authors: Moh Lan Yap / Thomas Klose / Fumio Arisaka / Jeffrey A Speir / David Veesler / Andrei Fokine / Michael G Rossmann / Abstract: Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation ...Bacteriophage T4 consists of a head for protecting its genome and a sheathed tail for inserting its genome into a host. The tail terminates with a multiprotein baseplate that changes its conformation from a "high-energy" dome-shaped to a "low-energy" star-shaped structure during infection. Although these two structures represent different minima in the total energy landscape of the baseplate assembly, as the dome-shaped structure readily changes to the star-shaped structure when the virus infects a host bacterium, the dome-shaped structure must have more energy than the star-shaped structure. Here we describe the electron microscopy structure of a 3.3-MDa in vitro-assembled star-shaped baseplate with a resolution of 3.8 Å. This structure, together with other genetic and structural data, shows why the high-energy baseplate is formed in the presence of the central hub and how the baseplate changes to the low-energy structure, via two steps during infection. Thus, the presence of the central hub is required to initiate the assembly of metastable, high-energy structures. If the high-energy structure is formed and stabilized faster than the low-energy structure, there will be insufficient components to assemble the low-energy structure. | ||||||
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 | 5hx2.cif.gz | 750.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hx2.ent.gz | 572.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hx2_validation.pdf.gz | 852.6 KB | Display | wwPDB validaton report |
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Full document | 5hx2_full_validation.pdf.gz | 998.2 KB | Display | |
Data in XML | 5hx2_validation.xml.gz | 134 KB | Display | |
Data in CIF | 5hx2_validation.cif.gz | 200.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/5hx2 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hx2 | HTTPS FTP |
-Related structure data
Related structure data | 8064MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: C6 (6 fold cyclic)) |
-Components
#1: Protein | Mass: 119336.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 7 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19061 | ||||||
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#2: Protein | Mass: 38041.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 8 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19062 #3: Protein | Mass: 74492.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 6 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19060 #4: Protein | | Mass: 22990.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 53 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16011 #5: Protein | Mass: 66281.680 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 10 / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10928 |
-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: In vitro assembled hubless T4 baseplate / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 3.3 MDa / Experimental value: NO |
Source (natural) | Organism: Enterobacteria phage T4 (virus) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET29 |
Buffer solution | pH: 8 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400-mesh copper CF-1.2/1.3-4C / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: CF-1.2/1.3-4C |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Details: Plunged into liquid ethane (GATAN CRYOPLUNGE 3). |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38168 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3740 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 7.6 sec. / Electron dose: 35 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1725 |
Image scans | Width: 7676 / Height: 7420 / Movie frames/image: 38 / Used frames/image: 3-38 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 69920 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45607 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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