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- EMDB-2244: Cryo-electron microscopy of phirsl1 jumbo phage -

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Basic information

Entry
Database: EMDB / ID: EMD-2244
TitleCryo-electron microscopy of phirsl1 jumbo phage
Map dataReconstruction of the helical trunk of phirsl1 tail. A Bfactor of -538 has been applied to the reconstruction as well as a soft-edged mask.
Sample
  • Sample: phirsl1 helical portion of the tail
  • Protein or peptide: Tail tube protein
  • Protein or peptide: Tail sheath protein
KeywordsJumbo bacteriophage / phiRSL1 / Ralstonia solanacearum / cryo-electron microscopy / icosahedral capsid / helical tail / T6SS
Function / homologyTail sheath protein
Function and homology information
Biological speciesRalstonia phage RSL1 (virus)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 9.6 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) releaseDec 26, 2012-
Map releaseFeb 20, 2013-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2244.png

Downloads & links

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Map

FileDownload / File: emd_2244.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the helical trunk of phirsl1 tail. A Bfactor of -538 has been applied to the reconstruction as well as a soft-edged mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 120 pix.
= 271.2 Å		2.26 Å/pix.
x 120 pix.
= 271.2 Å		2.26 Å/pix.
x 120 pix.
= 271.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.02692472 - 0.0357494
Average (Standard dev.)0.00069069 (±0.00452792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin0-3-5
Dimensions120120120
Spacing120120120
CellA=B=C: 271.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z271.200271.200271.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS-30-5
NC/NR/NS120120120
D min/max/mean-0.0270.0360.001

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Supplemental data

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Sample components

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Entire : phirsl1 helical portion of the tail

EntireName: phirsl1 helical portion of the tail
Components
  • Sample: phirsl1 helical portion of the tail
  • Protein or peptide: Tail tube protein
  • Protein or peptide: Tail sheath protein

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Supramolecule #1000: phirsl1 helical portion of the tail

SupramoleculeName: phirsl1 helical portion of the tail / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 1 / Details: UNP B2ZY00 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Ralstonia phage RSL1 (virus)
Molecular weightTheoretical: 18 KDa

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Macromolecule #2: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 2 / Details: UNP B2ZXZ8 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Ralstonia phage RSL1 (virus)
Molecular weightTheoretical: 68 KDa
SequenceInterPro: Tail sheath protein

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

DetailsProjection matching was done with SPIDER. IHRSR was used for helical parameters search and application.
Final reconstructionApplied symmetry - Helical parameters - Δz: 37.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.04 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, IHRSR
CTF correctionDetails: each particle

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