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- EMDB-8484: Bacteriophage G -

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Basic information

Entry
Database: EMDB / ID: 8484
TitleBacteriophage G
Map dataBacteriophage G
Samplebacteriophage G:
virus
Sourcebacteriophage G (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 15 Å resolution
AuthorsHua J / Huet A / Lopez CA / Toropova K / Pope WH / Duda RL / Hendrix RW / Conway JF
CitationJournal: MBio / Year: 2017
Title: Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold.
Authors: Jianfei Hua / Alexis Huet / Carlos A Lopez / Katerina Toropova / Welkin H Pope / Robert L Duda / Roger W Hendrix / James F Conway
Abstract: Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages ...Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages with double-stranded DNA genomes of at least 200,000 bp. We explored the mechanism leading to increased capsid and genome sizes by characterizing structures of several jumbophage capsids and the DNA packaged within them. Capsid structures determined for six jumbophages were consistent with the canonical phage HK97 fold, and three had capsid geometries with novel triangulation numbers (T=25, T=28, and T=52). Packaged DNA (chromosome) sizes were larger than the genome sizes, indicating that all jumbophages use a head-full DNA packaging mechanism. For two phages (PAU and G), the sizes appeared very much larger than their genome length. We used two-dimensional DNA gel electrophoresis to show that these two DNAs migrated abnormally due to base modifications and to allow us to calculate their actual chromosome sizes. Our results support a ratchet model of capsid and genome coevolution whereby mutations lead to increased capsid volume and allow the acquisition of additional genes. Once the added genes and larger capsid are established, mutations that restore the smaller size are disfavored. A large family of viruses share the same fold of the capsid protein as bacteriophage HK97, a virus that infects bacteria. Members of this family use different numbers of the capsid protein to build capsids of different sizes. Here, we examined the structures of extremely large capsids and measured their DNA content relative to the sequenced genome lengths, aiming to understand the process that increases size. We concluded that mutational changes leading to larger capsids become locked in by subsequent changes to the genome organization.
DateDeposition: Nov 29, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Nov 1, 2017 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8484.map.gz (map file in CCP4 format, 868328 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
601 pix
3.58 Å/pix.
= 2151.58 Å
601 pix
3.58 Å/pix.
= 2151.58 Å
601 pix
3.58 Å/pix.
= 2151.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.58 Å
Density
Contour Level:7.0 (by author), 7 (movie #1):
Minimum - Maximum-19.817001000000001 - 32.442999999999998
Average (Standard dev.)0.56182224 (3.909054)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions601601601
Origin0.0.0.
Limit600.600.600.
Spacing601601601
CellA=B=C: 2151.5798 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.583.583.58
M x/y/z601601601
origin x/y/z0.0000.0000.000
length x/y/z2151.5802151.5802151.580
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS601601601
D min/max/mean-19.81732.4430.562

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Supplemental data

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Sample components

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Entire bacteriophage G

EntireName: bacteriophage G / Number of components: 1

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Component #1: virus, bacteriophage G

VirusName: bacteriophage G / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: bacteriophage G (bacteriophage)
Source (natural)Host Species: Bacillus megaterium (bacteria)
Shell #1Name of element: capsid / Diameter: 1600.0 Å / T number(triangulation number): 52

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: OTHER / Temperature: 293 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 5000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 204 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 344
3D reconstructionResolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL

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