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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, Made by UCSF CHIMERA

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

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

Supplemental images

emd-1900.jpg
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

PDB-3ixw

PDB-3ixv

EMDB-5617

EMDB-5044
List of similar structure data about Omokage system
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 ( map file in CCP4 format, 4002 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
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

emd-1900.jpg
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 SO163
Image Acquisition
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 at 0.5 cut-off
Single Particle
Number of Projections15171
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

PDB-2x8k
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