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Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection.

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.00848698, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.00848698, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1269
TitleStructure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
Mapccp4 map of the tip of the bacteriophage spp1
SampleTip of the Tail of the bacteriophage SPP1
AuthorsPlisson C, White HE, Auzat I, Sao-jose C, Lhuillier S, Tavares P, Orlova EV
DateDeposition: 2006-09-21, Header release: 2006-09-22, Map release: 2007-09-07, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.00848698, Imaged by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.00848698, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleEMBO J., Vol. 26, Issue 15, Page 3720-3728, Year 2007
TitleStructure of bacteriophage SPP1 tail reveals trigger for DNA ejection.
AuthorsCelia Plisson, Helen E White, Isabelle Auzat, Amineh Zafarani, Carlos São-José, Sophie Lhuillier, Paulo Tavares, Elena V Orlova
School of Crystallography, Birkbeck College, University of London, London, UK.
KeywordsBacteriophages (genetics), DNA, Viral (chemistry), Microscopy, Electron
LinksPubMed: 17611601, DOI: 10.1038/sj.emboj.7601786, PMC: PMC1949002
Map
Fileemd_1269.map.gz ( map file in CCP4 format, 3251 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
3.3 A/pix
= 429. A
80 pix
3.3 A/pix
= 264. A
80 pix
3.3 A/pix
= 264. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.00819 (by author), 0.008487 (movie #1):
Minimum - Maximum: -0.00608738 - 0.15806589
Average (Standard dev.): 0.00082439 (0.00736948)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions8080130
Origin818161
Limit160160190
Spacing8080130
Unit CellA: 264 A, B: 264 A, C: 429 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.3 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.33.33.3
M x/y/z8080130
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000429.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS818161
NC/NR/NS8080130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0060.1580.001
Annotation Detailsccp4 map of the tip of the bacteriophage spp1
Supplement
Images
Images
Sample
NameTip of the Tail of the bacteriophage SPP1
Number of Components2
DetailsThe total number of proteins that compose the tail Tip is still under investigation.
Component #1: protein - gp19.1
Scientific nameinterface tail-tip
Common Namegp19.1
Experimental Mass0.0285 MDa
Scientific Name of SpeciesBacillus phage SPP1
Common Name of SpeciesBacteriophage SPP1
NCBI taxonomy10724
Recombinant expressionNo
Component #2: protein - gp21
Scientific nametip fiber
Common Namegp21
Experimental Mass0.123 MDa
Scientific Name of SpeciesBacillus phage SPP1
Common Name of SpeciesBacteriophage SPP1
NCBI taxonomy10724
Recombinant expressionNo
Experiment
Sample Preparation
Staining3.5 microliter of sample was applied onto carbon-coated copper grids, which were glow-discharged for 30 seconds. The sample was left for 1-2 minutes on the grids before blotting and staining with a solution of 2% uranyl acetate.
Specimen Support Details300 mesh copper grid
Specimen Stateparticle
BufferDetails: 100 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2
pH: 7.5
Vitrification
Cryogen NameNONE
Imaging
MicroscopeFEI TECNAI 12
DetailsLow Dose Imaging
Electron Gun
Electron SourceTUNGSTEN HAIRPIN
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 42000, Calibrated: 43475
Astigmatismobjective lens astigmatism was corrected at 150,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 2000 nm
Specimen Holder
HolderGatan single tilt negative stain holder
ModelOTHER
Temperature298 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Number of Digital Images20
Sampling Size7
Od Range2.5
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareIMAGIC
DetailsThe 3D reconstruction has been caried out using a C3 symmetry and the exact-filter back projection method.
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections364
Applied SymmetryC3 (3 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1269.xml (7.7 KB)
Map dataemd_1269.map.gz (124.6 KB)
Images1269.gif (18.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1269
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 3.8 MB
Session file for UCSF-Chimera, 20.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 3.6 MB
Session file for UCSF-Chimera, 20.3 KB