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- EMDB-4150: Structure of the baseplate of Siphophage J-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-4150
TitleStructure of the baseplate of Siphophage J-1
Map dataThis is the baseplate of siphophage J-1 (Lactobacillus casei BL23 phage) with a part of the tail
Sample
  • Complex: virion's baseplate
Biological speciesLactobacillus phage J-1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsCambillau C / Spinelli S / Dieterle ME / Piuri M
CitationJournal: Mol Microbiol / Year: 2017
Title: Evolved distal tail carbohydrate binding modules of Lactobacillus phage J-1: a novel type of anti-receptor widespread among lactic acid bacteria phages.
Authors: Maria-Eugenia Dieterle / Silvia Spinelli / Irina Sadovskaya / Mariana Piuri / Christian Cambillau /
Abstract: Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding ...Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell-wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J-1 that infects Lactobacillus casei seemed to lack one. It has been shown that the phage J-1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared with 'classical' Dits. The first insertion is similar to carbohydrate-binding modules (CBMs), whereas the second insertion remains undocumented. Here, we determined the structure of the second insertion and found it also similar to several CBMs. Expressed insertion CBM2, but not CBM1, binds to L. casei cells and neutralize phage attachment to the bacterial cell wall and the isolated and purified CWPS of L. casei BL23 prevents CBM2 attachment to the host. Electron microscopy single particle reconstruction of the J-1 virion baseplate revealed that CBM2 is projected at the periphery of Dit to optimally bind the CWPS receptor. Taken together, these results identify J-1 evolved Dit as the phage RBP.
History
DepositionOct 17, 2016-
Header (metadata) releaseNov 23, 2016-
Map releaseNov 30, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4150.png

Downloads & links

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Map

FileDownload / File: emd_4150.map.gz / Format: CCP4 / Size: 214.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the baseplate of siphophage J-1 (Lactobacillus casei BL23 phage) with a part of the tail
Voxel sizeX=Y=Z: 4.83 Å
Density
Contour LevelBy AUTHOR: 0.0305 / Movie #1: 0.0305
Minimum - Maximum-0.25784045 - 0.49923614
Average (Standard dev.)-0.0017591693 (±0.08419317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions383838
Spacing383838
CellA=B=C: 183.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.834.834.83
M x/y/z383838
origin x/y/z0.0000.0000.000
length x/y/z183.540183.540183.540
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS383838
D min/max/mean-0.2580.499-0.002

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Supplemental data

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Sample components

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Entire : virion's baseplate

EntireName: virion's baseplate
Components
  • Complex: virion's baseplate

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Supramolecule #1: virion's baseplate

SupramoleculeName: virion's baseplate / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Lactobacillus phage J-1 (virus)

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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
StainingType: NEGATIVE / Material: 1% uranyl acetate
Details: stained with 10 microL of 1% uranyl acetate for 30 sec
DetailsThe baseplate was boxed at the virion's tip

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 865
Initial angle assignmentType: OTHER / Software - Name: Xmipp (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: Xmipp (ver. 3.1)
Final angle assignmentType: OTHER / Software - Name: Xmipp (ver. 3.1)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp (ver. 3.1) / Number images used: 865

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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