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- EMDB-4678: The cryo-EM structure of the connector of the mature bacteriophag... -

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Basic information

Entry
Database: EMDB / ID: EMD-4678
TitleThe cryo-EM structure of the connector of the mature bacteriophage phi29
Map data
SampleBacillus phage phi29 (bacteriophage):
virus / Portal protein
Function / homologyPortal protein Gp10 superfamily / Portal protein Gp10 / Phage Connector (GP10) / viral portal complex / viral DNA genome packaging / viral genome ejection through host cell envelope, short tail mechanism / viral procapsid / RNA binding / Portal protein
Function and homology information
Biological speciesBacillus phage phi29 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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.
Validation ReportPDB-ID: 6qyj

SummaryFull reportAbout validation report
DateDeposition: Mar 9, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 19, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.33
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qyj
  • Surface level: 3.33
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4678.map.gz / Format: CCP4 / Size: 713.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 572 pix.
= 743.6 Å
1.3 Å/pix.
x 572 pix.
= 743.6 Å
1.3 Å/pix.
x 572 pix.
= 743.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 3.33 / Movie #1: 3.33
Minimum - Maximum-0.41685185 - 42.791289999999996
Average (Standard dev.)0.005217688 (±0.27057835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions572572572
Spacing572572572
CellA=B=C: 743.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z572572572
origin x/y/z0.0000.0000.000
length x/y/z743.600743.600743.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS572572572
D min/max/mean-0.41742.7910.005

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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, Portal protein

ProteinName: Portal protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 35.917293 kDa
SourceSpecies: Bacillus phage phi29 (bacteriophage)

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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: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 36730
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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