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- EMDB-2246: Cryo-electron microscopy of phirsl1 jumbo phage -

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Basic information

Entry
Database: EMDB / ID: EMD-2246
TitleCryo-electron microscopy of phirsl1 jumbo phage
Map dataReconstruction of phirsl1 baseplate
Sample
  • Sample: phirsl1 baseplate
  • Protein or peptide: phirsl1
KeywordsJumbo bacteriophage / phiRSL1 / Ralstonia solanacearum / cryo-electron microscopy / icosahedral capsid / helical tail / T6SS
Biological speciesRalstonia phage RSL1 (virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 21.0 Å
AuthorsEffantin G / Hamasaki R / Kawasaki T / Bacia M / Moriscot C / Weissenhorn W / Yamada T / Schoehn G
CitationJournal: Structure / Year: 2013
Title: Cryo-electron microscopy three-dimensional structure of the jumbo phage ΦRSL1 infecting the phytopathogen Ralstonia solanacearum.
Authors: Grégory Effantin / Ryosuke Hamasaki / Takeru Kawasaki / Maria Bacia / Christine Moriscot / Winfried Weissenhorn / Takashi Yamada / Guy Schoehn /
Abstract: ϕRSL1 jumbo phage belongs to a new class of viruses within the Myoviridae family. Here, we report its three-dimensional structure determined by electron cryo microscopy. The icosahedral capsid, the ...ϕRSL1 jumbo phage belongs to a new class of viruses within the Myoviridae family. Here, we report its three-dimensional structure determined by electron cryo microscopy. The icosahedral capsid, the tail helical portion, and the complete tail appendage were reconstructed separately to resolutions of 9 Å, 9 Å, and 28 Å, respectively. The head is rather complex and formed by at least five different proteins, whereas the major capsid proteins resemble those from HK97, despite low sequence conservation. The helical tail structure demonstrates its close relationship to T4 sheath proteins and provides evidence for an evolutionary link of the inner tail tube to the bacterial type VI secretion apparatus. Long fibers extend from the collar region, and their length is consistent with reaching the host cell surface upon tail contraction. Our structural analyses indicate that ϕRSL1 is an unusual member of the Myoviridae that employs conserved protein machines related to different phages and bacteria.
History
DepositionDec 18, 2012-
Header (metadata) releaseJan 23, 2013-
Map releaseFeb 20, 2013-
UpdateFeb 20, 2013-
Current statusFeb 20, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2246.png

Downloads & links

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Map

FileDownload / File: emd_2246.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of phirsl1 baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.52 Å/pix.
x 180 pix.
= 813.6 Å		4.52 Å/pix.
x 180 pix.
= 813.6 Å		4.52 Å/pix.
x 180 pix.
= 813.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.05785812 - 0.07104485
Average (Standard dev.)-0.00000244 (±0.00410206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 813.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.524.524.52
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z813.600813.600813.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0580.071-0.000

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Supplemental data

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Sample components

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Entire : phirsl1 baseplate

EntireName: phirsl1 baseplate
Components
  • Sample: phirsl1 baseplate
  • Protein or peptide: phirsl1

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Supramolecule #1000: phirsl1 baseplate

SupramoleculeName: phirsl1 baseplate / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: phirsl1

MacromoleculeName: phirsl1 / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Ralstonia phage RSL1 (virus)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 50 mM Tris-HCl [pH 7.5], 100 mM NaCl, 10 mM MgSO4
StainingType: NEGATIVE
Details: Four microliters of the bacteriophage sample (~0.1 mg/ml) were loaded between the mica-carbon interface. The sample was stained using 2% ammonium molybdate pH 7.5 and air-dried.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59000
DateFeb 25, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 52 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 5.295 µm / Nominal defocus min: 1.355 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 1228

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