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- EMDB-1779: EM structure of bacteriophage SPP1 distal tail protein (GP 19.1):... -

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Basic information

Entry
Database: EMDB / ID: EMD-1779
TitleEM structure of bacteriophage SPP1 distal tail protein (GP 19.1): a baseplate hub paradigm in gram positive infecting phages
Map dataEM map of Dit (GP19.1) from SPP1 Bacteriophage
Sample
  • Sample: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
  • Protein or peptide: GP19.1
KeywordsDit / GP 19.1 / SPP1 / Bacteriophage
Biological speciesBacillus phage SPP1 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 21.5 Å
AuthorsVeesler D / Robin G / Lichiere J / Auzat I / Tavares P / Bron P / Campanacci V / Cambillau C
CitationJournal: J Biol Chem / Year: 2010
Title: Crystal structure of bacteriophage SPP1 distal tail protein (gp19.1): a baseplate hub paradigm in gram-positive infecting phages.
Authors: David Veesler / Gautier Robin / Julie Lichière / Isabelle Auzat / Paulo Tavares / Patrick Bron / Valérie Campanacci / Christian Cambillau /
Abstract: Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most ...Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.
History
DepositionSep 3, 2010-
Header (metadata) releaseSep 24, 2010-
Map releaseDec 21, 2010-
UpdateDec 21, 2010-
Current statusDec 21, 2010Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd1779.jpg

Downloads & links

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Map

FileDownload / File: emd_1779.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of Dit (GP19.1) from SPP1 Bacteriophage
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.19 Å/pix.
x 128 pix.
= 280.32 Å		2.19 Å/pix.
x 128 pix.
= 280.32 Å		2.19 Å/pix.
x 128 pix.
= 280.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0 / Movie #1: 10
Minimum - Maximum-20.881900000000002 - 52.165300000000002
Average (Standard dev.)-0.000000000131899 (±5.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-63-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 280.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.192.192.19
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z280.320280.320280.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-64-63-64
NC/NR/NS128128128
D min/max/mean-20.88252.165-0.000

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Supplemental data

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Sample components

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Entire : GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage

EntireName: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
Components
  • Sample: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
  • Protein or peptide: GP19.1

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Supramolecule #1000: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage

SupramoleculeName: GP 19.1 protein from B. subtilis phage SPP1 Bacteriophage
type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Dodecameric / Number unique components: 1
Molecular weightExperimental: 325.629 KDa / Theoretical: 28.489 KDa
Method: Molar mass and hydrodynamic radius determination by SEC, MALS,UV,QELS and RI.

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Macromolecule #1: GP19.1

MacromoleculeName: GP19.1 / type: protein_or_peptide / ID: 1 / Name.synonym: Dit / Number of copies: 12 / Oligomeric state: Dodecameric / Recombinant expression: Yes
Source (natural)Organism: Bacillus phage SPP1 (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

Concentration0.010 mg/mL
BufferpH: 7.5 / Details: 10 mM HEPES, 150 mM NaCl
StainingType: NEGATIVE
Details: 3 microLitres of freshly prepared protein were applied on a glow-discharged carbon-coated grid. The excess of Dit solution was blotted and 4 microliters of 1% Uranyl- Acetate was applied ...Details: 3 microLitres of freshly prepared protein were applied on a glow-discharged carbon-coated grid. The excess of Dit solution was blotted and 4 microliters of 1% Uranyl- Acetate was applied twice on the grid and incubated for 1 min. Grids were then dried and kept in a desiccator cabinet until use
GridDetails: 400-Mesh Carbon-Coated Copper Grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsLow-dose imaging
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 10 µm / Number real images: 8 / Average electron dose: 18 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45710 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V / Number images used: 9027

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