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- EMDB-11179: Head of Semi-jumbo phage RP13 -

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Basic information

Entry
Database: EMDB / ID: EMD-11179
TitleHead of Semi-jumbo phage RP13
Map data
Sample
  • Virus: Ralstonia phage p12J (virus)
Biological speciesRalstonia phage p12J (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsNeumann E / Kawasaki T / Effantin G / Estrozi L / Chatchawankanphanich O / Yamada T / Schoehn G
CitationJournal: J Gen Virol / Year: 2020
Title: 3D structure of three jumbo phage heads.
Authors: Emmanuelle Neumann / Takeru Kawasaki / Grégory Effantin / Leandro F Estrozi / Orawan Chatchawankanphanich / Takashi Yamada / Guy Schoehn /
Abstract: Jumbo phages are bacteriophages that carry more than 200 kbp of DNA. In this study we characterized two jumbo phages (ΦRSL2 and ΦXacN1) and one semi-jumbo phage (ΦRP13) at the structural level by ...Jumbo phages are bacteriophages that carry more than 200 kbp of DNA. In this study we characterized two jumbo phages (ΦRSL2 and ΦXacN1) and one semi-jumbo phage (ΦRP13) at the structural level by cryo-electron microscopy. Focusing on their capsids, three-dimensional structures of the heads at resolutions ranging from 16 to 9 Å were calculated. Based on these structures we determined the geometrical basis on which the icosahedral capsids of these phages are constructed, which includes the accessory and decorative proteins that complement them. A triangulation number novel to (ΦRP13; =21) was discovered as well as two others, which are more common for jumbo phages (=27 and =28). Based on one of the structures we also provide evidence that accessory or decorative proteins are not a prerequisite for maintaining the structural integrity of very large capsids.
History
DepositionJun 15, 2020-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11179.png

Downloads & links

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Map

FileDownload / File: emd_11179.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.88 Å/pix.
x 340 pix.
= 1319.2 Å		3.88 Å/pix.
x 340 pix.
= 1319.2 Å		3.88 Å/pix.
x 340 pix.
= 1319.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.05
Minimum - Maximum-0.09833436 - 0.2700427
Average (Standard dev.)0.008251629 (±0.026082514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-339-339-339
Dimensions340340340
Spacing340340340
CellA=B=C: 1319.2001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.883.883.88
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z1319.2001319.2001319.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-339-339-339
NC/NR/NS340340340
D min/max/mean-0.0980.2700.008

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Supplemental data

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Sample components

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Entire : Ralstonia phage p12J

EntireName: Ralstonia phage p12J (virus)
Components
  • Virus: Ralstonia phage p12J (virus)

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Supramolecule #1: Ralstonia phage p12J

SupramoleculeName: Ralstonia phage p12J / type: virus / ID: 1 / Parent: 0 / Details: RP13 - In deposition / NCBI-ID: 247080 / Sci species name: Ralstonia phage p12J / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ralstonia (bacteria)
Virus shellShell ID: 1 / Name: RP13 / Diameter: 1140.0 Å / T number (triangulation number): 21

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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: 7.5
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1311
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: RELION / Number images used: 669
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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