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- EMDB-7559: Bacteriophage A511 baseplate in post-host attachment state (urea-... -

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Basic information

Entry
Database: EMDB / ID: 7559
TitleBacteriophage A511 baseplate in post-host attachment state (urea-induced)
Map dataBacteriophage A511 in post-host attachment contracted state (urea-induced)
SampleListeria virus A511:
virus
SourceListeria virus A511 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 14 Å resolution
AuthorsGuerrero-Ferreira R
CitationJournal: EMBO J. / Year: 2019
Title: Structure and transformation of bacteriophage A511 baseplate and tail upon infection of  cells.
Authors: Ricardo C Guerrero-Ferreira / Mario Hupfeld / Sergey Nazarov / Nicholas Mi Taylor / Mikhail M Shneider / Jagan M Obbineni / Martin J Loessner / Takashi Ishikawa / Jochen Klumpp / Petr G Leiman
Abstract: Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and ...Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.
DateDeposition: Mar 16, 2018 / Header (metadata) release: Mar 28, 2018 / Map release: Jan 23, 2019 / Last update: Feb 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

emd_7559.png

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Map

Fileemd_7559.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
2.27 Å/pix.
= 681. Å		300 pix
2.27 Å/pix.
= 681. Å		300 pix
2.27 Å/pix.
= 681. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.27 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.231116 - 0.330529
Average (Standard dev.)0.002388366 (0.03250877)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 681.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.272.272.27
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z681.000681.000681.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2310.3310.002

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Supplemental data

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Sample components

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Entire Listeria virus A511

EntireName: Listeria virus A511
Details: Propagated in Listeria ivanovii strain WSLC 3009 (SV 5)
Number of components: 1

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Component #1: virus, Listeria virus A511

VirusName: Listeria virus A511 / Class: VIRION
Details: Propagated in Listeria ivanovii strain WSLC 3009 (SV 5)
Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Listeria virus A511 (bacteriophage)
Source (natural)Host Species: Listeria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: SM buffer: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 8 mM MgSO4
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI EAGLE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 9218
3D reconstructionSoftware: RELION / Resolution: 14 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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