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- EMDB-10913: Structure of the phage STP1 host adhesion device (baseplate) by n... -

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Basic information

Entry
Database: EMDB / ID: EMD-10913
TitleStructure of the phage STP1 host adhesion device (baseplate) by negative staining
Map dataStructure of the phage STP1 host adhesion device (baseplate) by negative staining
Sample
  • Virus: Streptococcus phage STP1 (virus)
Biological speciesStreptococcus phage STP1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsLavelle K / Goulet A / McDonnell B / Spinelli S / van Sinderen D / Mahony J / Cambillau C
Funding support Ireland, France, 3 items
OrganizationGrant numberCountry
Science Foundation Ireland15/SIRG/3430 Ireland
French National Research AgencyANR-10-INSB-05-01 France
Science Foundation Ireland13/IA/1953 Ireland
CitationJournal: Microb Biotechnol / Year: 2020
Title: Revisiting the host adhesion determinants of Streptococcus thermophilus siphophages.
Authors: Katherine Lavelle / Adeline Goulet / Brian McDonnell / Silvia Spinelli / Douwe van Sinderen / Jennifer Mahony / Christian Cambillau /
Abstract: Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus ...Available 3D structures of bacteriophage modules combined with predictive bioinformatic algorithms enabled the identification of adhesion modules in 57 siphophages infecting Streptococcus thermophilus (St). We identified several carbohydrate-binding modules (CBMs) in so-called evolved distal tail (Dit) and tail-associated lysozyme (Tal) proteins of St phage baseplates. We examined the open reading frame (ORF) downstream of the Tal-encoding ORF and uncovered the presence of a putative p2-like receptor-binding protein (RBP). A 21 Å resolution electron microscopy structure of the baseplate of cos-phage STP1 revealed the presence of six elongated electron densities, surrounding the core of the baseplate, that harbour the p2-like RBPs at their tip. To verify the functionality of these modules, we expressed GFP- or mCherry-coupled Tal and putative RBP CBMs and observed by fluorescence microscopy that both modules bind to their corresponding St host, the putative RBP CBM with higher affinity than the Tal-associated one. The large number of CBM functional domains in St phages suggests that they play a contributory role in the infection process, a feature that we previously described in lactococcal phages and beyond, possibly representing a universal feature of the siphophage host-recognition apparatus.
History
DepositionApr 24, 2020-
Header (metadata) releaseJun 24, 2020-
Map releaseJun 24, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0172
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10913.png

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Map

FileDownload / File: emd_10913.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the phage STP1 host adhesion device (baseplate) by negative staining
Voxel sizeX=Y=Z: 4.87 Å
Density
Contour LevelBy AUTHOR: 0.0172 / Movie #1: 0.0172
Minimum - Maximum-0.0755889 - 0.11639657
Average (Standard dev.)-0.0027668474 (±0.013437231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 487.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.874.874.87
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z487.000487.000487.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0760.116-0.003

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Supplemental data

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Sample components

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Entire : Streptococcus phage STP1

EntireName: Streptococcus phage STP1 (virus)
Components
  • Virus: Streptococcus phage STP1 (virus)

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Supramolecule #1: Streptococcus phage STP1

SupramoleculeName: Streptococcus phage STP1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2041508 / Sci species name: Streptococcus phage STP1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Streptococcus thermophilus (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
Component:
ConcentrationFormula
100.0 mMNaClSodium chloride
50.0 mMTris-HClTris
10.0 mMMgSO4
StainingType: NEGATIVE / Material: uranyl acetate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: OTHER / Average electron dose: 20.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3324
CTF correctionSoftware - Name: RELION (ver. 3.0.8)
Startup modelType of model: OTHER
Details: The initial model was generated by ab initio reconstruction using the stochastic gradient descent method in Relion.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 1051

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