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Structure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation

by single particle reconstruction, at 22 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.5, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.5, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1699
TitleStructure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation
MapThis is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2
SampleP2 baseplate wild-type
Keywordsp2, baseplate, phage, EM
AuthorsSciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichiere J, van Heel M, Campanacci V, Moineau S, Cambillau C
DateDeposition: 2010-02-05, Header release: 2010-03-10, Map release: 2010-03-10, Last update: 2010-06-01
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.5, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.5, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 15, Page 6852-7, Year 2010
TitleStructure of lactococcal phage p2 baseplate and its mechanism of activation.
AuthorsGiuliano Sciara, Cecilia Bebeacua, Patrick Bron, Denise Tremblay, Miguel Ortiz-Lombardia, Julie Lichière, Marin van Heel, Valérie Campanacci, Sylvain Moineau, Christian Cambillau
Architecture et Fonction des Macromolécules Biologiques, UMR 6098 Centre National de la Recherche Scientifique and Universités d'Aix-Marseille I & II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.
KeywordsBacteriophage P2 (metabolism), Binding Sites, Calcium (chemistry), Cations, Cryoelectron Microscopy (methods), Crystallography, X-Ray (methods), Escherichia coli (metabolism), Lactococcus lactis (virology), Microscopy, Electron (methods), Molecular Conformation, Molecular Sequence Data, Open Reading Frames, Protein Binding, Protein Conformation, Viral Tail Proteins (chemistry)
LinksDOI: 10.1073/pnas.1000232107, PubMed: 20351260, PMC: PMC2872406
Map
Fileemd_1699.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
4.64 A/pix
= 593.92 A
128 pix
4.64 A/pix
= 593.92 A
128 pix
4.64 A/pix
= 593.92 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum: -7.12447 - 15.0054
Average (Standard dev.): 0.0791262 (0.812704)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-63-64
Limit636463
Spacing128128128
Unit CellA= B= C: 593.92 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.64 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.644.644.64
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z593.920593.920593.920
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-63-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-7.12415.0050.079
Annotation DetailsThis is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2
Supplement
Images
Images
Sample
NameP2 baseplate wild-type
Number of Components1
Oligomeric StateHomohexamer
Theoretical Mass1MDa
Experimental Mass1MDa
Component #1: protein - P2 baseplate
Scientific nameP2 baseplate
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesLactococcus phage p2
NCBI taxonomy254252
Recombinant expressionNo
Experiment
Sample Preparation
StainingSample was incubated on glow-discharged grid for approximately one minute. 2% uranyl acetate was applied onto the sample and left for about 30 seconds.
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG/UT
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 38000
Astigmatismcorrected at 200,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus500 nm - 1500 nm
Specimen Holder
HolderRoom Temperature
ModelOTHER
Tilt Angle0 degrees - 0 degrees
Camera
Image Acquisition
#1
Number of Digital Images1000
Sampling Size2.32
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmExact-filter back projections
Euler Angles DetailsIMAGIC
SoftwareIMAGIC-5
CTF CorrectionCCD Images
DetailsInitial map calculated with class averages. Final map calculated after projection matching refinement.
Resolution By Author22 A
Resolution MethodFSC 1/2 BIT
Single Particle
Number of Projections9486
Applied SymmetryC6 (6 fold cyclic)
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Data from EMDB
Header (meta data in XML format)emd-1699.xml (7 KB)
Map dataemd_1699.map.gz (828.7 KB)
Images3d_p2baseplate.png (80.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1699
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 25.5 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, 25.5 KB