EMDB-1699: Structure of Lactococcal Phage p2 Baseplate and its Me...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1699
Title	Structure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation
Map	This 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
Sample	P2 baseplate wild-type
Keywords	p2, baseplate, phage, EM
Authors	Sciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichiere J, van Heel M, Campanacci V, Moineau S, Cambillau C
Date	Deposition: 2010-02-05, Header release: 2010-03-10, Map release: 2010-03-10, Last update: 2010-06-01
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 1.5, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.5, Made by UCSF CHIMERA
Supplemental images	3d_p2basepla...
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1706 Cite PDB-2wzp Cite PDB-2x53 Cite PDB-2x54 Cite PDB-2x5a Cite Cite: data citing same article
Similar strucutres (beta)	Diagram PDB-2ymh EMDB-1647 EMDB-2299 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 15, Page 6852-7, Year 2010
Title	Structure of lactococcal phage p2 baseplate and its mechanism of activation.
Authors	Giuliano 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.
Keywords	Bacteriophage P2 (metabolism), Binding Sites, Calcium (chemistry, 7440-70-2), 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)
Links	DOI: 10.1073/pnas.1000232107, PubMed: 20351260, PMC: PMC2872406

Map

File

EMD-1699.map ( map file in CCP4 format, 8390 KB )

Projections & Slices

Size of images:

Axes	Z (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:	1.5 (by author), 1.5 (movie #1):
Minimum - Maximum:	-7.12447 - 15.0054
Average (Standard dev.):	0.0791262 (0.812704)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	128	128	128
Origin	-64	-63	-64
Limit	63	64	63
Spacing	128	128	128

Unit Cell

A= B= C: 593.92 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 4.64 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	4.64	4.64	4.64
M x/y/z	128	128	128
origin x/y/z	0.000	0.000	0.000
length x/y/z	593.920	593.920	593.920
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	0	0	0
NX/NY/NZ	121	121	121
MAP C/R/S	1	2	3
start NC/NR/NS	-63	-64	-64
NC/NR/NS	128	128	128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-7.124	15.005	0.079

Annotation Details

This 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	3d_p2basepla...

Sample
Name	P2 baseplate wild-type
Number of Components	1
Oligomeric State	Homohexamer
Theoretical Mass	1MDa
Experimental Mass	1MDa
Component #1: protein - P2 baseplate
Scientific name	P2 baseplate
Oligomeric Details	Hexamer
Number of Copies	6
Scientific Name of Species	Lactococcus phage p2
NCBI taxonomy	254252
Recombinant expression	No

Experiment
Sample Preparation
Staining	Sample 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 State	particle
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI/PHILIPS CM200FEG/UT
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	10 e/A**2
Illumination Mode	SPOT SCAN
Lens
Magnification	Nominal: 38000
Astigmatism	corrected at 200,000 times magnification
Nominal Cs	2.2 mm
Imaging Mode	BRIGHT FIELD
Defocus	500 nm - 1500 nm
Specimen Holder
Holder	Room Temperature
Model	OTHER
Tilt Angle	0 degrees - 0 degrees
Camera
Image Acquisition
Number of Digital Images	1000
Sampling Size	2.32

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Exact-filter back projections
Euler Angles Details	IMAGIC
Software	IMAGIC-5
CTF Correction	CCD Images
Details	Initial map calculated with class averages. Final map calculated after projection matching refinement.
Resolution By Author	22 A
Resolution Method	FSC at half-bit cut-off
Single Particle
Number of Projections	9486

Download

Data from EMDB

Header (meta data in XML format)

emd-1699.xml (6.9 KB)

Map data

emd_1699.map.gz (828.7 KB)

Images

3d_p2baseplate.png (80.9 KB)

FTP directory

ftp://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