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- EMDB-11224: negative staining 3D reconstruction of p2 virion baseplate in act... -

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Basic information

Entry
Database: EMDB / ID: EMD-11224
Titlenegative staining 3D reconstruction of p2 virion baseplate in activated conformation (3D class with open Tal trimer)
Map datanegative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with open Tal trimer)
Sample
  • Virus: Lactococcus virus P2
Biological speciesLactococcus virus P2
Methodsingle particle reconstruction / negative staining / Resolution: 35.4 Å
AuthorsSpinelli S / Cambillau C / Goulet A
CitationJournal: Viruses / Year: 2020
Title: Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism.
Authors: Silvia Spinelli / Denise Tremblay / Sylvain Moineau / Christian Cambillau / Adeline Goulet /
Abstract: Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated ...Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected.
History
DepositionJun 26, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateAug 26, 2020-
Current statusAug 26, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11224.png

Downloads & links

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Map

FileDownload / File: emd_11224.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with open Tal trimer)
Voxel sizeX=Y=Z: 3.46 Å
Density
Contour LevelBy AUTHOR: 3.1 / Movie #1: 3.1
Minimum - Maximum-16.463089 - 21.24631
Average (Standard dev.)0.0000000025 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 885.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.463.463.46
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z885.760885.760885.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-16.46321.2460.000

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Supplemental data

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Sample components

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Entire : Lactococcus virus P2

EntireName: Lactococcus virus P2
Components
  • Virus: Lactococcus virus P2

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Supramolecule #1: Lactococcus virus P2

SupramoleculeName: Lactococcus virus P2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 254252 / Sci species name: Lactococcus virus P2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: uranyl acetate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 293
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 35.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 193
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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