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- EMDB-1900: Cryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1900
TitleCryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex
Map dataCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
Sample
  • Sample: SPP1 bacteriophage gp19.1-gp21(1-552) complex
  • Protein or peptide: gp19.1
  • Protein or peptide: gp21(1-552)
KeywordsBacteriophage / SPP1 / Tail tip / gp19.1 / Dit / gp21 / Tal / tail adsorption apparatus / infection mechanism
Biological speciesunidentified phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsGoulet A / Lai-Kee-Him J / Veesler D / Auzat I / Robin G / Shepherd DA / Ashcroft AE / Richard E / Lichiere J / Tavares P ...Goulet A / Lai-Kee-Him J / Veesler D / Auzat I / Robin G / Shepherd DA / Ashcroft AE / Richard E / Lichiere J / Tavares P / Cambillau C / Bron P
CitationJournal: J Biol Chem / Year: 2011
Title: The opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages.
Authors: Adeline Goulet / Joséphine Lai-Kee-Him / David Veesler / Isabelle Auzat / Gautier Robin / Dale A Shepherd / Alison E Ashcroft / Eric Richard / Julie Lichière / Paulo Tavares / Christian ...Authors: Adeline Goulet / Joséphine Lai-Kee-Him / David Veesler / Isabelle Auzat / Gautier Robin / Dale A Shepherd / Alison E Ashcroft / Eric Richard / Julie Lichière / Paulo Tavares / Christian Cambillau / Patrick Bron /
Abstract: The SPP1 siphophage uses its long non-contractile tail and tail tip to recognize and infect the Gram-positive bacterium Bacillus subtilis. The tail-end cap and its attached tip are the critical ...The SPP1 siphophage uses its long non-contractile tail and tail tip to recognize and infect the Gram-positive bacterium Bacillus subtilis. The tail-end cap and its attached tip are the critical components for host recognition and opening of the tail tube for genome exit. In the present work, we determined the cryo-electron microscopic (cryo-EM) structure of a complex formed by the cap protein gp19.1 (Dit) and the N terminus of the downstream protein of gp19.1 in the SPP1 genome, gp21(1-552) (Tal). This complex assembles two back-to-back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack. Remarkably, one gp21(1-552) trimer displays a "closed" conformation, whereas the second is "open" delineating a central channel. The two conformational states dock nicely into the EM map of the SPP1 cap domain, respectively, before and after DNA release. Moreover, the open/closed conformations of gp19.1-gp21(1-552) are consistent with the structures of the corresponding proteins in the siphophage p2 baseplate, where the Tal protein (ORF16) attached to the ring of Dit (ORF15) was also found to adopt these two conformations. Therefore, the present contribution allowed us to revisit the SPP1 tail distal-end architectural organization. Considering the sequence conservation among Dit and the N-terminal region of Tal-like proteins in Gram-positive-infecting Siphoviridae, it also reveals the Tal opening mechanism as a hallmark of siphophages probably involved in the generation of the firing signal initiating the cascade of events that lead to phage DNA release in vivo.
History
DepositionMay 24, 2011-
Header (metadata) releaseMay 27, 2011-
Map releaseJun 10, 2011-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 60
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1900.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
Voxel sizeX=Y=Z: 4.38 Å
Density
Contour LevelBy AUTHOR: 60.0 / Movie #1: 60
Minimum - Maximum0.0 - 100.0
Average (Standard dev.)51.789200000000001 (±3.06874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 438 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.384.384.38
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z438.000438.000438.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-50-49-50
NC/NR/NS100100100
D min/max/mean0.000100.00051.789

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Supplemental data

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Sample components

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Entire : SPP1 bacteriophage gp19.1-gp21(1-552) complex

EntireName: SPP1 bacteriophage gp19.1-gp21(1-552) complex
Components
  • Sample: SPP1 bacteriophage gp19.1-gp21(1-552) complex
  • Protein or peptide: gp19.1
  • Protein or peptide: gp21(1-552)

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Supramolecule #1000: SPP1 bacteriophage gp19.1-gp21(1-552) complex

SupramoleculeName: SPP1 bacteriophage gp19.1-gp21(1-552) complex / type: sample / ID: 1000
Oligomeric state: This complex assembles two back-to- back stacked gp19.1 ring hexamers, interacting loosely, and two gp21(1-552) trimers interacting with gp19.1 at both ends of the stack
Number unique components: 2
Molecular weightExperimental: 730 KDa / Method: SEC, MALS, RI, UV, QELS

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Macromolecule #1: gp19.1

MacromoleculeName: gp19.1 / type: protein_or_peptide / ID: 1 / Name.synonym: Dit / Recombinant expression: Yes
Source (natural)Organism: unidentified phage (virus) / synonym: Dit

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Macromolecule #2: gp21(1-552)

MacromoleculeName: gp21(1-552) / type: protein_or_peptide / ID: 2 / Name.synonym: Tal / Recombinant expression: Yes
Source (natural)Organism: unidentified phage (virus) / synonym: Tal

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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

Concentration0.07 mg/mL
BufferpH: 7.5 / Details: 10 mM HEPES, 150 mM NaCl
GridDetails: Quantifoil R 2/2 grids
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 102.15 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification instrument: Cryoplunge CP3 gatan / Method: Blot for 2s, both sides

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45591 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: Omega JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
TemperatureAverage: 98.15 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
DetailsImages recorded on a JEOL 2200FS
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: 100 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC / Number images used: 15171

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Atomic model buiding 1

Initial modelPDB ID:
DetailsThe initial fit was done by manual docking followed by refinement using the (fit in map) Chimera plugging
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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