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Open data
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Basic information
Entry | Database: PDB / ID: 6qvk | ||||||||||||
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Title | The cryo-EM structure of bacteriophage phi29 prohead | ||||||||||||
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![]() | VIRUS / bacteriophage / phi29 / prohead | ||||||||||||
Function / homology | ![]() viral capsid, fiber / viral procapsid / T=3 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Xu, J. / Gui, M. / Xiang, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural assembly of the tailed bacteriophage ϕ29. Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang / ![]() ![]() ![]() Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration. | ||||||||||||
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 | ![]() | 25.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4655MC ![]() 4662C ![]() 4677C ![]() 4678C ![]() 4679C ![]() 4680C ![]() 4681C ![]() 4682C ![]() 4683C ![]() 4684C ![]() 4685C ![]() 6qx7C ![]() 6qydC ![]() 6qyjC ![]() 6qymC ![]() 6qyyC ![]() 6qyzC ![]() 6qz0C ![]() 6qz9C ![]() 6qzfC 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: Protein | Mass: 49894.906 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 29642.361 Da / Num. of mol.: 165 / Source method: isolated from a natural source Details: the residue 118-281 is adapted from crystal structure of gp8.5 (PDB entry:3QC7). 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: Bacillus phage phi29 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: PRION |
Buffer solution | pH: 7.5 |
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: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18230 / Symmetry type: POINT |