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

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Basic information

Entry
Database: EMDB / ID: 1699
TitleStructure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation
Keywordsp2 / baseplate / phage / EM
SampleP2 baseplate wild-type
SourceLactococcus phage p2 / virus
Map dataThis 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
Methodsingle particle reconstruction, at 22 Å resolution
AuthorsSciara G / Bebeacua C / Bron P / Tremblay D / Ortiz-Lombardia M / Lichiere J / van Heel M / Campanacci V / Moineau S / Cambillau C
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 6852-6857

Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 6852-6857 StrPapers
Structure of lactococcal phage p2 baseplate and its mechanism of activation.
Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau

DateDeposition: Feb 5, 2010 / Header (metadata) release: Mar 10, 2010 / Map release: Mar 10, 2010 / Last update: Feb 5, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1699.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
4.64 Å/pix.
= 593.92 Å
128 pix
4.64 Å/pix.
= 593.92 Å
128 pix
4.64 Å/pix.
= 593.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.64 Å
Density
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum-7.12447 - 15.0054
Average (Standard dev.)0.0791262 (0.812704)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-63-64
Limit636463
Spacing128128128
CellA=B=C: 593.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS-63-64-64
NC/NR/NS128128128
D min/max/mean-7.12415.0050.079

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Supplemental data

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Sample components

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Entire P2 baseplate wild-type

EntireName: P2 baseplate wild-type / Number of components: 1 / Oligomeric State: Homohexamer
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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Component #1: protein, P2 baseplate

ProteinName: P2 baseplate / a.k.a: P2 baseplate / Oligomeric Details: Hexamer / Recombinant expression: No / Number of Copies: 6
SourceSpecies: Lactococcus phage p2 / virus

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Experimental details

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Sample preparation

Specimen stateparticle
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.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG/UT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 38000 X (nominal) / Astigmatism: corrected at 200,000 times magnification / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1500 nm
Specimen HolderHolder: Room Temperature / Model: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 1000 / Sampling size: 2.32 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 9486 / Applied symmetry: C6 (6 fold cyclic)
3D reconstructionAlgorithm: Exact-filter back projections / Euler angles: IMAGIC / Software: IMAGIC-5 / CTF correction: CCD Images
Details: Initial map calculated with class averages. Final map calculated after projection matching refinement.
Resolution: 22 Å / Resolution method: FSC 1/2 BIT

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