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- PDB-6qyd: Cryo-EM structure of the head in mature bacteriophage phi29 -

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Basic information

Entry
Database: PDB / ID: 6qyd
TitleCryo-EM structure of the head in mature bacteriophage phi29
Components
  • Capsid fiber protein
  • Major capsid protein
KeywordsVIRUS / bacteriophage / cryo-EM / mature virus
Function / homology
Function and homology information


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
Bacteriophage B103, Gp8, head fibre / Head fiber protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Capsid fiber protein / Major capsid protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu, J.W. / Wang, D.H. / Gui, M. / Xiang, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)20166YFA0501100 China
National Natural Science Foundation of China31470721 China
National Natural Science Foundation of China31861143027 China
National Natural Science Foundation of China21827810 China
CitationJournal: Nat Commun / Year: 2019
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
DepositionMar 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
1A: Major capsid protein
1B: Major capsid protein
1C: Major capsid protein
1D: Major capsid protein
1E: Major capsid protein
1F: Major capsid protein
2A: Major capsid protein
2B: Major capsid protein
2C: Major capsid protein
2D: Major capsid protein
2E: Major capsid protein
3A: Major capsid protein
3B: Major capsid protein
3C: Major capsid protein
3D: Major capsid protein
3E: Major capsid protein
3F: Major capsid protein
4A: Major capsid protein
4B: Major capsid protein
4C: Major capsid protein
4D: Major capsid protein
4E: Major capsid protein
4F: Major capsid protein
5A: Major capsid protein
5B: Major capsid protein
5C: Major capsid protein
5D: Major capsid protein
5E: Major capsid protein
5F: Major capsid protein
6A: Major capsid protein
6B: Major capsid protein
6C: Major capsid protein
6D: Major capsid protein
6E: Major capsid protein
6F: Major capsid protein
7A: Major capsid protein
7B: Major capsid protein
7C: Major capsid protein
7D: Major capsid protein
7E: Major capsid protein
8A: Major capsid protein
8B: Major capsid protein
8C: Major capsid protein
8D: Major capsid protein
8E: Major capsid protein
8F: Major capsid protein
9A: Major capsid protein
1G: Major capsid protein
1H: Major capsid protein
1I: Major capsid protein
1J: Major capsid protein
1K: Major capsid protein
1L: Major capsid protein
2F: Major capsid protein
2G: Major capsid protein
2H: Major capsid protein
2I: Major capsid protein
2J: Major capsid protein
3G: Major capsid protein
3H: Major capsid protein
3I: Major capsid protein
3J: Major capsid protein
3K: Major capsid protein
3L: Major capsid protein
4G: Major capsid protein
4H: Major capsid protein
4I: Major capsid protein
4J: Major capsid protein
4K: Major capsid protein
4L: Major capsid protein
5G: Major capsid protein
5H: Major capsid protein
5I: Major capsid protein
5J: Major capsid protein
5K: Major capsid protein
5L: Major capsid protein
6G: Major capsid protein
6H: Major capsid protein
6I: Major capsid protein
6J: Major capsid protein
6K: Major capsid protein
6L: Major capsid protein
7F: Major capsid protein
7G: Major capsid protein
7H: Major capsid protein
7I: Major capsid protein
7J: Major capsid protein
8G: Major capsid protein
8H: Major capsid protein
8I: Major capsid protein
8J: Major capsid protein
8K: Major capsid protein
8L: Major capsid protein
9B: Major capsid protein
1M: Major capsid protein
1N: Major capsid protein
1O: Major capsid protein
1P: Major capsid protein
1Q: Major capsid protein
1R: Major capsid protein
2K: Major capsid protein
2L: Major capsid protein
2M: Major capsid protein
2N: Major capsid protein
2O: Major capsid protein
3M: Major capsid protein
3N: Major capsid protein
3O: Major capsid protein
3P: Major capsid protein
3Q: Major capsid protein
3R: Major capsid protein
4M: Major capsid protein
4N: Major capsid protein
4O: Major capsid protein
4P: Major capsid protein
4Q: Major capsid protein
4R: Major capsid protein
5M: Major capsid protein
5N: Major capsid protein
5O: Major capsid protein
5P: Major capsid protein
5Q: Major capsid protein
5R: Major capsid protein
6M: Major capsid protein
6N: Major capsid protein
6O: Major capsid protein
6P: Major capsid protein
6Q: Major capsid protein
6R: Major capsid protein
7K: Major capsid protein
7L: Major capsid protein
7M: Major capsid protein
7N: Major capsid protein
7O: Major capsid protein
8M: Major capsid protein
8N: Major capsid protein
8O: Major capsid protein
8P: Major capsid protein
8Q: Major capsid protein
8R: Major capsid protein
9C: Major capsid protein
1S: Major capsid protein
1T: Major capsid protein
1U: Major capsid protein
1V: Major capsid protein
1W: Major capsid protein
1X: Major capsid protein
2P: Major capsid protein
2Q: Major capsid protein
2R: Major capsid protein
2S: Major capsid protein
2T: Major capsid protein
3S: Major capsid protein
3T: Major capsid protein
3U: Major capsid protein
3V: Major capsid protein
3W: Major capsid protein
3X: Major capsid protein
4S: Major capsid protein
4T: Major capsid protein
4U: Major capsid protein
4V: Major capsid protein
4W: Major capsid protein
4X: Major capsid protein
5S: Major capsid protein
5T: Major capsid protein
5U: Major capsid protein
5V: Major capsid protein
5W: Major capsid protein
5X: Major capsid protein
6S: Major capsid protein
6T: Major capsid protein
6U: Major capsid protein
6V: Major capsid protein
6W: Major capsid protein
6X: Major capsid protein
7P: Major capsid protein
7Q: Major capsid protein
7R: Major capsid protein
7S: Major capsid protein
7T: Major capsid protein
8S: Major capsid protein
8T: Major capsid protein
8U: Major capsid protein
8V: Major capsid protein
8W: Major capsid protein
8X: Major capsid protein
9D: Major capsid protein
1Y: Major capsid protein
1Z: Major capsid protein
1a: Major capsid protein
1b: Major capsid protein
1c: Major capsid protein
1d: Major capsid protein
2U: Major capsid protein
2V: Major capsid protein
2W: Major capsid protein
2X: Major capsid protein
2Y: Major capsid protein
3Y: Major capsid protein
3Z: Major capsid protein
3a: Major capsid protein
3b: Major capsid protein
3c: Major capsid protein
3d: Major capsid protein
4Y: Major capsid protein
4Z: Major capsid protein
4a: Major capsid protein
4b: Major capsid protein
4c: Major capsid protein
4d: Major capsid protein
5Y: Major capsid protein
5Z: Major capsid protein
5a: Major capsid protein
5b: Major capsid protein
5c: Major capsid protein
5d: Major capsid protein
6Y: Major capsid protein
6Z: Major capsid protein
6a: Major capsid protein
6b: Major capsid protein
6c: Major capsid protein
6d: Major capsid protein
7U: Major capsid protein
7V: Major capsid protein
7W: Major capsid protein
7X: Major capsid protein
7Y: Major capsid protein
8Y: Major capsid protein
8Z: Major capsid protein
8a: Major capsid protein
8b: Major capsid protein
8c: Major capsid protein
8d: Major capsid protein
9E: Major capsid protein
1e: Capsid fiber protein
1f: Capsid fiber protein
1g: Capsid fiber protein
1h: Capsid fiber protein
2Z: Capsid fiber protein
2a: Capsid fiber protein
2b: Capsid fiber protein
2c: Capsid fiber protein
2d: Capsid fiber protein
3e: Capsid fiber protein
3f: Capsid fiber protein
3g: Capsid fiber protein
3h: Capsid fiber protein
4e: Capsid fiber protein
4f: Capsid fiber protein
5e: Capsid fiber protein
5f: Capsid fiber protein
6e: Capsid fiber protein
6f: Capsid fiber protein
6g: Capsid fiber protein
6h: Capsid fiber protein
7Z: Capsid fiber protein
7a: Capsid fiber protein
7b: Capsid fiber protein
7c: Capsid fiber protein
7d: Capsid fiber protein
8e: Capsid fiber protein
8f: Capsid fiber protein
8g: Capsid fiber protein
8h: Capsid fiber protein
8i: Capsid fiber protein
8j: Capsid fiber protein
9F: Capsid fiber protein
1i: Capsid fiber protein
1j: Capsid fiber protein
1k: Capsid fiber protein
1l: Capsid fiber protein
2e: Capsid fiber protein
2f: Capsid fiber protein
2g: Capsid fiber protein
2h: Capsid fiber protein
2i: Capsid fiber protein
3i: Capsid fiber protein
3j: Capsid fiber protein
3k: Capsid fiber protein
3l: Capsid fiber protein
4g: Capsid fiber protein
4h: Capsid fiber protein
5g: Capsid fiber protein
5h: Capsid fiber protein
6i: Capsid fiber protein
6j: Capsid fiber protein
6k: Capsid fiber protein
6l: Capsid fiber protein
7e: Capsid fiber protein
7f: Capsid fiber protein
7g: Capsid fiber protein
7h: Capsid fiber protein
7i: Capsid fiber protein
8k: Capsid fiber protein
8l: Capsid fiber protein
8m: Capsid fiber protein
8n: Capsid fiber protein
8o: Capsid fiber protein
8p: Capsid fiber protein
9G: Capsid fiber protein
1m: Capsid fiber protein
1n: Capsid fiber protein
1o: Capsid fiber protein
1p: Capsid fiber protein
2j: Capsid fiber protein
2k: Capsid fiber protein
2l: Capsid fiber protein
2m: Capsid fiber protein
2n: Capsid fiber protein
3m: Capsid fiber protein
3n: Capsid fiber protein
3o: Capsid fiber protein
3p: Capsid fiber protein
4i: Capsid fiber protein
4j: Capsid fiber protein
5i: Capsid fiber protein
5j: Capsid fiber protein
6m: Capsid fiber protein
6n: Capsid fiber protein
6o: Capsid fiber protein
6p: Capsid fiber protein
7j: Capsid fiber protein
7k: Capsid fiber protein
7l: Capsid fiber protein
7m: Capsid fiber protein
7n: Capsid fiber protein
8q: Capsid fiber protein
8r: Capsid fiber protein
8s: Capsid fiber protein
8t: Capsid fiber protein
8u: Capsid fiber protein
8v: Capsid fiber protein
9H: Capsid fiber protein
1q: Capsid fiber protein
1r: Capsid fiber protein
1s: Capsid fiber protein
1t: Capsid fiber protein
2o: Capsid fiber protein
2p: Capsid fiber protein
2q: Capsid fiber protein
2r: Capsid fiber protein
2s: Capsid fiber protein
3q: Capsid fiber protein
3r: Capsid fiber protein
3s: Capsid fiber protein
3t: Capsid fiber protein
4k: Capsid fiber protein
4l: Capsid fiber protein
5k: Capsid fiber protein
5l: Capsid fiber protein
6q: Capsid fiber protein
6r: Capsid fiber protein
6s: Capsid fiber protein
6t: Capsid fiber protein
7o: Capsid fiber protein
7p: Capsid fiber protein
7q: Capsid fiber protein
7r: Capsid fiber protein
7s: Capsid fiber protein
8w: Capsid fiber protein
8x: Capsid fiber protein
8y: Capsid fiber protein
8z: Capsid fiber protein
9K: Capsid fiber protein
9L: Capsid fiber protein
9I: Capsid fiber protein
1u: Capsid fiber protein
1v: Capsid fiber protein
1w: Capsid fiber protein
1x: Capsid fiber protein
2t: Capsid fiber protein
2u: Capsid fiber protein
2v: Capsid fiber protein
2w: Capsid fiber protein
2x: Capsid fiber protein
3u: Capsid fiber protein
3v: Capsid fiber protein
3w: Capsid fiber protein
3x: Capsid fiber protein
4m: Capsid fiber protein
4n: Capsid fiber protein
5m: Capsid fiber protein
5n: Capsid fiber protein
6u: Capsid fiber protein
6v: Capsid fiber protein
6w: Capsid fiber protein
6x: Capsid fiber protein
7t: Capsid fiber protein
7u: Capsid fiber protein
7v: Capsid fiber protein
7w: Capsid fiber protein
7x: Capsid fiber protein
9M: Capsid fiber protein
9N: Capsid fiber protein
9O: Capsid fiber protein
9P: Capsid fiber protein
9Q: Capsid fiber protein
9R: Capsid fiber protein
9J: Capsid fiber protein


Theoretical massNumber of molelcules
Total (without water)16,616,292400
Polymers16,616,292400
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Major capsid protein / Gene product 8 / gp8 / Major head protein / Protein p8


Mass: 49894.906 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus) / References: UniProt: P13849
#2: Protein ...
Capsid fiber protein / Gene product 8.5 / gp8.5 / Head fiber protein / Protein p8.5


Mass: 29642.361 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Source: (natural) Bacillus phage phi29 (virus) / References: UniProt: B3VMP4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus virus phi29 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus virus phi29
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36730 / Symmetry type: POINT

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