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- EMDB-11180: Head reconstruction of full jumbo phage XacN1 -

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Basic information

Entry
Database: EMDB / ID: EMD-11180
TitleHead reconstruction of full jumbo phage XacN1
Map dataFull Head Reconstruction of jumbo phage XacN1
Sample
  • Virus: Xanthomonas citri (bacteria)
Biological speciesXanthomonas citri (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 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 16, 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11180.png

Downloads & links

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Map

FileDownload / File: emd_11180.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull Head Reconstruction of jumbo phage XacN1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.88 Å/pix.
x 420 pix.
= 1629.6 Å		3.88 Å/pix.
x 420 pix.
= 1629.6 Å		3.88 Å/pix.
x 420 pix.
= 1629.6 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-0.13803439 - 0.25809422
Average (Standard dev.)0.006145869 (±0.02558859)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 1629.6001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.883.883.88
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z1629.6001629.6001629.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1380.2580.006

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Supplemental data

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Sample components

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Entire : Xanthomonas citri

EntireName: Xanthomonas citri (bacteria)
Components
  • Virus: Xanthomonas citri (bacteria)

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Supramolecule #1: Xanthomonas citri

SupramoleculeName: Xanthomonas citri / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 346 / Sci species name: Xanthomonas citri / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Xanthomonas citri (bacteria)
Virus shellShell ID: 1 / Name: XacN1 / Diameter: 1395.0 Å / T number (triangulation number): 28

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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
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
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1775
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: RELION / Number images used: 1149
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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