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

by single particle reconstruction, at 26 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 60, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 60, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1900
TitleCryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex
MapCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
SampleSPP1 bacteriophage gp19.1-gp21(1-552) complex
KeywordsBacteriophage, SPP1, Tail tip, gp19.1, Dit, gp21, Tal, tail adsorption apparatus, infection mechanism
AuthorsGoulet 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
DateDeposition: 2011-05-24, Header release: 2011-05-27, Map release: 2011-06-10, Last update: 2011-09-09
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 60, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 60, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleJ. Biol. Chem., Vol. 286, Issue 28, Page 25397-405, Year 2011
TitleThe opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages.
AuthorsAdeline 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
Centre de Biochimie Structurale, INSERM UMR 1054/CNRS UMR 5048 and Universités Montpellier I & II, 29 rue de Navacelles, Montpellier 34090, France.
KeywordsBacillus subtilis (genetics), Genome, Viral (physiology), Protein Structure, Tertiary, Siphoviridae (physiology), Viral Structural Proteins (genetics), Virus Attachment
LinksDOI: 10.1074/jbc.M111.243360, PubMed: 21622577, PMC: PMC3137110
Map
Fileemd_1900.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.38 A/pix
= 438. A
100 pix
4.38 A/pix
= 438. A
100 pix
4.38 A/pix
= 438. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:60 (by author), 60 (movie #1):
Minimum - Maximum: 0 - 100
Average (Standard dev.): 51.7892 (3.06874)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-49-50-50
Limit504949
Spacing100100100
Unit CellA= B= C: 438 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.38 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-50-49-50
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean0.000100.00051.789
Annotation DetailsCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
Supplement
Images
Images
Sample
NameSPP1 bacteriophage gp19.1-gp21(1-552) complex
Number of Components2
Oligomeric StateThis 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
Mass-estimation MethodSEC, MALS, RI, UV, QELS
Experimental Mass0.73MDa
Component #1: protein - Dit
Scientific namegp19.1
Common NameDit
Scientific Name of Speciesunidentified phage
Common Name of SpeciesDit
NCBI taxonomy38018
Recombinant expressionYes
Component #2: protein - Tal
Scientific namegp21(1-552)
Common NameTal
Scientific Name of Speciesunidentified phage
Common Name of SpeciesTal
NCBI taxonomy38018
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Conc0.07 mg/ml
Specimen Support DetailsQuantifoil R 2/2 grids
Specimen Stateparticle
BufferDetails: 10 mM HEPES, 150 mM NaCl
pH: 7.5
Vitrification
MethodBlot for 2s, both sides
Cryogen NameETHANE
DetailsVitrification instrument: Cryoplunge CP3 gatan
Humidity90
InstrumentGATAN CRYOPLUNGE 3
Temperature102.15 Kelvin
Imaging
MicroscopeJEOL 2200FS
DetailsImages recorded on a JEOL 2200FS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 45591
AstigmatismObjective lens astigmatism was corrected at 200,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1400 nm - 2500 nm
Energy FilterEnergy Filter: Omega JEOL , Energy Window: 0-20 eV
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Temperature98.15 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images100
Sampling Size10
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareIMAGIC
CTF CorrectionEach particle
Resolution By Author26 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections15171
Applied SymmetryD3 (2*3 fold dihedral)
Atomic Model Fitting
Model #0
DetailsThe initial fit was done by manual docking followed by refinement using the (fit in map) Chimera plugging
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID2X8K
Download
Data from EMDB
Header (meta data in XML format)emd-1900.xml (8.3 KB)
Map dataemd_1900.map.gz (3 MB)
Imagesemd-1900.jpg (75.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1900
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.8 KB