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- EMDB-4683: The cryo-EM structure of the tail knob in genome empited bacterio... -

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Entry
Database: EMDB / ID: EMD-4683
TitleThe cryo-EM structure of the tail knob in genome empited bacteriophage phi29
Map data
SampleBacillus phage phi29 (bacteriophage)
  • virus
  • the tail knob protein (gp9, gene product 9) in bacteriophage phi29
Biological speciesBacillus phage phi29 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsXu J / Wang D / Gui M / Xiang Y
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.
DateDeposition: Mar 10, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_4683.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 540 pix.
= 734.4 Å
1.36 Å/pix.
x 540 pix.
= 734.4 Å
1.36 Å/pix.
x 540 pix.
= 734.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.42865524 - 4.2171893
Average (Standard dev.)0.0010754344 (±0.039019596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-268-268-268
Dimensions540540540
Spacing540540540
CellA=B=C: 734.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z734.400734.400734.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-268-268-268
NC/NR/NS540540540
D min/max/mean-0.4294.2170.001

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Supplemental data

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Sample components

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Entire Bacillus phage phi29

EntireName: Bacillus phage phi29 (bacteriophage) / Number of components: 2

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Component #1: virus, Bacillus phage phi29

VirusName: Bacillus phage phi29 / Class: PRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Bacillus phage phi29 (bacteriophage)

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Component #2: protein, the tail knob protein (gp9, gene product 9) in bacteriop...

ProteinName: the tail knob protein (gp9, gene product 9) in bacteriophage phi29
Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 31478
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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