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- EMDB-21695: Full phage G capsid cryoEM structure at 6.1 Angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-21695
TitleFull phage G capsid cryoEM structure at 6.1 Angstrom resolution
Map data
Sample
  • Virus: Bacillus virus G
Function / homology: / Phage capsid / Phage capsid family / Gp26 / Gp27
Function and homology information
Biological speciesBacillus virus G
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsGonzalez B / Monroe L / Kunpeng L / Yan R / Wright E / Walter T / Kihara D / Weintraub SE / Julie AT / Philip S / Jiang W
CitationJournal: J Mol Biol / Year: 2020
Title: Phage G Structure at 6.1 Å Resolution, Condensed DNA, and Host Identity Revision to a Lysinibacillus.
Authors: Brenda González / Lyman Monroe / Kunpeng Li / Rui Yan / Elena Wright / Thomas Walter / Daisuke Kihara / Susan T Weintraub / Julie A Thomas / Philip Serwer / Wen Jiang /
Abstract: Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and ...Phage G has the largest capsid and genome of any known propagated phage. Many aspects of its structure, assembly, and replication have not been elucidated. Herein, we present the dsDNA-packed and empty phage G capsid at 6.1 and 9 Å resolution, respectively, using cryo-EM for structure determination and mass spectrometry for protein identification. The major capsid protein, gp27, is identified and found to share the HK97-fold universally conserved in all previously solved dsDNA phages. Trimers of the decoration protein, gp26, sit on the 3-fold axes and are thought to enhance the interactions of the hexameric capsomeres of gp27, for other phages encoding decoration proteins. Phage G's decoration protein is longer than what has been reported in other phages, and we suspect the extra interaction surface area helps stabilize the capsid. We identified several additional capsid proteins, including a candidate for the prohead protease responsible for processing gp27. Furthermore, cryo-EM reveals a range of partially full, condensed DNA densities that appear to have no contact with capsid shell. Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megaterium: identity of host proteins in our mass spectrometry analyses, genome sequence of the phage G host, and host range of phage G.
History
DepositionApr 14, 2020-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.21
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.21
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wkk
  • Surface level: 2.21
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wkk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21695.png

Downloads & links

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Map

FileDownload / File: emd_21695.map.gz / Format: CCP4 / Size: 7.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 1280 pix.
= 2229.76 Å		1.74 Å/pix.
x 1280 pix.
= 2229.76 Å		1.74 Å/pix.
x 1280 pix.
= 2229.76 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.21 / Movie #1: 2.21
Minimum - Maximum-6.725375 - 8.556715
Average (Standard dev.)0.024299111 (±0.51442003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-640-640-640
Dimensions128012801280
Spacing128012801280
CellA=B=C: 2229.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7421.7421.742
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z2229.7602229.7602229.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-6.7258.5570.024

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Supplemental data

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Mask #1

Fileemd_21695_msk_1.map
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Mask #2

Fileemd_21695_msk_2.map
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Half map: #1

Fileemd_21695_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_21695_half_map_2.map
Projections & Slices
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Sample components

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Entire : Bacillus virus G

EntireName: Bacillus virus G
Components
  • Virus: Bacillus virus G

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Supramolecule #1: Bacillus virus G

SupramoleculeName: Bacillus virus G / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1084719 / Sci species name: Bacillus virus G / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Diameter: 1600.0 Å / T number (triangulation number): 52

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 0.01 M Tris-Cl (pH 7.4), 0.01 M MgSO4, 6% polyethylene glycol MW 3350
VitrificationCryogen name: ETHANE / Chamber humidity: 65 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
Details: Three microliters of phage G sample was deposited on a 400 mesh Ted Pella ultrathin lacey carbon grid and incubated for 30 minutes in a humid chamber on ice. The grid was then washed with 10 ...Details: Three microliters of phage G sample was deposited on a 400 mesh Ted Pella ultrathin lacey carbon grid and incubated for 30 minutes in a humid chamber on ice. The grid was then washed with 10 microliters of 0.2 TM buffer. Using a Gatan CP3 plunger, the grid was then blotted for 9 seconds with Whatman 1 filter paper at 65% humidity, then plunge-frozen in liquid ethane. The plunge-frozen, phage G grid was then imaged using a Titan Krios equipped with a K2 detector in super-resolution mode at the Purdue Cryo-EM Facility with a nominal magnification of 8,700 resulting in 1.742 Angstroms per pixel. A total of 375 movies was collected..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 375 / Average electron dose: 14.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 8700
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: jspr
Startup modelType of model: OTHER / Details: used jspr for initial modeling
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr
Details: Phage G's capsid was reconstructed with icosahedral symmetry
Number images used: 2564
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: jspr
FSC plot (resolution estimation)

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