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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: EMD-7559
TitleBacteriophage A511 baseplate in post-host attachment state (urea-induced)
Map dataBacteriophage A511 in post-host attachment contracted state (urea-induced)
Sample
  • Virus: Listeria virus A511
Biological speciesListeria virus A511
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
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.
History
DepositionMar 16, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseJan 23, 2019-
UpdateFeb 13, 2019-
Current statusFeb 13, 2019Processing site: RCSB / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7559.png

Downloads & links

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Map

FileDownload / File: emd_7559.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage A511 in post-host attachment contracted state (urea-induced)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.27 Å/pix.
x 300 pix.
= 681. Å		2.27 Å/pix.
x 300 pix.
= 681. Å		2.27 Å/pix.
x 300 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 LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.231116 - 0.330529
Average (Standard dev.)0.002388366 (±0.03250877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 681.0 Å
α=β=γ: 90.0 °

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
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
Components
  • Virus: Listeria virus A511

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Supramolecule #1: Listeria virus A511

SupramoleculeName: Listeria virus A511 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Propagated in Listeria ivanovii strain WSLC 3009 (SV 5)
NCBI-ID: 40523 / Sci species name: Listeria virus A511 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Listeria (bacteria)

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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
Details: SM buffer: 50 mM Tris-HCl, pH 7.5, 100 mM NaCl, 8 mM MgSO4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsSpecimen was dialyzed into SM buffer containing 2M urea prior to cryo-EM sample preparation

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10122
CTF correctionSoftware - Name: Xmipp
Startup modelType of model: OTHER / Details: Model generated using Spider software
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9218
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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