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- EMDB-11178: Jumbo Bacteriophage RSL2 - Full icosahedral capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-11178
TitleJumbo Bacteriophage RSL2 - Full icosahedral capsid
Map dataHead Reconstruction of the jumbo phage RSL2
Sample
  • Virus: Ralstonia virus RSL2
Biological speciesRalstonia virus RSL2
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 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) releaseOct 21, 2020-
Map releaseOct 21, 2020-
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: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11178.png

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Map

FileDownload / File: emd_11178.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHead Reconstruction of the jumbo phage RSL2
Voxel sizeX=Y=Z: 6.57 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.04725319 - 0.09838778
Average (Standard dev.)0.005600698 (±0.016237633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 1576.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.576.576.57
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z1576.8001576.8001576.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0470.0980.006

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Supplemental data

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Sample components

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Entire : Ralstonia virus RSL2

EntireName: Ralstonia virus RSL2
Components
  • Virus: Ralstonia virus RSL2

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Supramolecule #1: Ralstonia virus RSL2

SupramoleculeName: Ralstonia virus RSL2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1980925 / Sci species name: Ralstonia virus RSL2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ralstonia solanacearum MAFF 106603
Virus shellShell ID: 1 / Name: RSL2 Head / Diameter: 1390.0 Å / T number (triangulation number): 27

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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 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 499
Startup modelType of model: OTHER
Details: The initial 3D model of full RSL2 capsids has been calculated with the RIco software.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: RELION / Number images used: 250
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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