|Entry||Database: EMDB / ID: EMD-4677|
|Title||Cryo-EM structure of the head in mature bacteriophage phi29|
|Sample||Bacillus virus phi29 (bacteriophage):|
virus / Major capsid protein / Capsid fiber protein
|Function / homology|
Function and homology information
viral capsid, fiber / viral procapsid / T=3 icosahedral viral capsid / viral entry into host cell / virion attachment to host cell / identical protein binding
Bacterial Ig-like, group 2 / Bacteriophage B103, Gp8, head fibre / Bacterial Ig-like domain (group 2) / Head fiber protein
Capsid fiber protein / Major capsid protein
|Biological species||Bacillus virus phi29 (bacteriophage) / Bacteriophage phi-29 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.2 Å|
|Authors||Xu JW / Wang DH / Gui M / Xiang Y|
|Citation||Journal: 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.
|Validation Report||PDB-ID: 6qyd|
SummaryFull reportAbout validation report
|Date||Deposition: Mar 8, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4677.map.gz / Format: CCP4 / Size: 713.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2952 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Bacillus virus phi29
|Entire||Name: Bacillus virus phi29 (bacteriophage) / Number of components: 3|
-Component #1: virus, Bacillus virus phi29
|Virus||Name: Bacillus virus phi29 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Bacillus virus phi29 (bacteriophage)|
-Component #2: protein, Major capsid protein
|Protein||Name: Major capsid protein / Number of Copies: 235 / Recombinant expression: No|
|Mass||Theoretical: 49.894906 kDa|
|Source||Species: Bacteriophage phi-29 (bacteriophage)|
-Component #3: protein, Capsid fiber protein
|Protein||Name: Capsid fiber protein / Number of Copies: 165 / Recombinant expression: No|
|Mass||Theoretical: 29.642361 kDa|
|Source||Species: Bacteriophage phi-29 (bacteriophage)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 36730|
|3D reconstruction||Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
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