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The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.

by single particle reconstruction, at 16.4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.1, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.1, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1333
TitleThe structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
MapSixfold averaged tail of bacteriophage K1E
SampleSixfold averaged tail of bacteriophage K1E
AuthorsLeiman PG, Battisti AJ, Bowman VD, Stummeyer K, Muhlenhoff M, Gerardy-Schahn R, Scholl D, Molineux IJ
DateDeposition: 2007-03-06, Header release: 2007-03-06, Map release: 2007-07-18, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.1, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.1, Image by UCSF CHIMERA

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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 371, Issue 3, Page 836-49, Year 2007
TitleThe structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.
AuthorsPetr G Leiman, Anthony J Battisti, Valorie D Bowman, Katharina Stummeyer, Martina Mühlenhoff, Rita Gerardy-Schahn, Dean Scholl, Ian J Molineux
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
KeywordsBacterial Capsules (metabolism), Bacteriophages (chemistry), Biological Evolution, Capsid (chemistry), Cryoelectron Microscopy, DNA Packaging, DNA, Viral (chemistry), Escherichia coli (virology), Genome, Viral, Models, Molecular, Sequence Homology, Amino Acid, Species Specificity, Static Electricity, Viral Proteins (chemistry), Virion (chemistry)
LinksPII: S0022-2836(07)00756-5, DOI: 10.1016/j.jmb.2007.05.083, PubMed: 17585937
Map
Fileemd_1333.map.gz ( map file in CCP4 format, 21297 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
176 pix
2.98 A/pix
= 524.48 A
176 pix
2.98 A/pix
= 524.48 A
176 pix
2.98 A/pix
= 524.48 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.92, 1.1 (movie #1):
Minimum - Maximum: -8.55116 - 9.72964
Average (Standard dev.): 3.25921e-10 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions176176176
Origin-88-88-88
Limit878787
Spacing176176176
Unit CellA= B= C: 524.48 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.98 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.982.982.98
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z524.480524.480524.480
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-88-88-88
NC/NR/NS176176176
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-8.5519.7300.000
Annotation DetailsSixfold averaged tail of bacteriophage K1E
Supplement
Images
Images
Sample
NameSixfold averaged tail of bacteriophage K1E
Number of Components1
Experimental Mass8MDa
Theoretical Mass8MDa
Mass-estimation MethodPrimary sequence
Component #1: virus - phage K1E tail
Scientific nameEnterobacteria phage K1E
Common Namephage K1E tail
Theoretical Mass8 MDa
Experimental Mass8 MDa
Detailssixfold averaged
Scientific Name of SpeciesEnterobacteria phage K1E
Common Name of Speciesphage K1E tail
NCBI taxonomy344022
EmptyNo
EnvelopedNo
IsolateSPECIES
ClassVIRION
Natural SourceNCBI taxonomy: 562
Host Species: Escherichia coli
Host Category: BACTERIA(EUBACTERIA)
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Stainingnone
Specimen Support Detailsquantifoil grid
Specimen Stateparticle
BufferDetails: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 8 mM MgSO4
pH: 7.5
Vitrification
Cryogen NameETHANE
Humidity80
Temperature300 Kelvin
InstrumentFEI VITROBOT
DetailsVitrification instrument: Vitrobot
Imaging
MicroscopeFEI/PHILIPS CM300FEG/T
Date2005-05-10
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose25 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 45000, Calibrated: 47000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus700 nm - 3300 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Temperature100 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images122
Sampling Size7
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmweighted back-projection
SoftwareSpider
CTF CorrectionEach particle
Resolution By Author16.4 A
Resolution MethodFSC at 0.4 cut-off
Single Particle
Number of Projections6105
Applied SymmetryC6 (6 fold cyclic)
Download
Data from EMDB
Header (meta data in XML format)emd-1333.xml (7.5 KB)
Map dataemd_1333.map.gz (13.1 MB)
Images1333.gif (51.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1333
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 20.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 20.3 KB