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- EMDB-1900: Cryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex -

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Basic information

Entry
Database: EMDB / ID: 1900
TitleCryo-EM map of the SPP1 bacteriophage gp19.1-gp21(1-552) complex
KeywordsBacteriophage / SPP1 / Tail tip / gp19.1 / Dit / gp21 / Tal / tail adsorption apparatus / infection mechanism
SampleSPP1 bacteriophage gp19.1-gp21(1-552) complex
Sourceunidentified phage / virus / Dit, Tal
Map dataCCP4 Map file of Bacteriophage spp1 Dit-Tal complex
Methodsingle particle reconstruction, at 26 A resolution
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
CitationJ. Biol. Chem., 2011, 286, 25397-25405

J. Biol. Chem., 2011, 286, 25397-25405 StrPapers
The opening of the SPP1 bacteriophage tail, a prevalent mechanism in Gram-positive-infecting siphophages.
Adeline 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

DateDeposition: May 24, 2011 / Header (metadata) release: May 27, 2011 / Map release: Jun 10, 2011 / Last update: May 24, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 60
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1900.map.gz (map file in CCP4 format, 3908 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.38 A/pix
= 438. A
100 pix
4.38 A/pix
= 438. A
100 pix
4.38 A/pix
= 438. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.38 A
Density
Contour Level:60 (by author), 60 (movie #1):
Minimum - Maximum0 - 100
Average (Standard dev.)51.7892 (3.06874)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-49-50-50
Limit504949
Spacing100100100
CellA=B=C: 438 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean0.000100.00051.789

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Supplemental data

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Sample components

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Entire SPP1 bacteriophage gp19.1-gp21(1-552) complex

EntireName: SPP1 bacteriophage gp19.1-gp21(1-552) complex / Number of components: 2
Oligomeric State: This 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
MassExperimental: 730 kDa / Measured by: SEC, MALS, RI, UV, QELS

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Component #1: protein, gp19.1

ProteinName: gp19.1 / a.k.a: Dit / Recombinant expression: Yes
SourceSpecies: unidentified phage / virus / Dit

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Component #2: protein, gp21(1-552)

ProteinName: gp21(1-552) / a.k.a: Tal / Recombinant expression: Yes
SourceSpecies: unidentified phage / virus / Tal

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.07 mg/ml / Buffer solution: 10 mM HEPES, 150 mM NaCl / pH: 7.5
Support filmQuantifoil R 2/2 grids
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 102.15 K / Humidity: 90 % / Method: Blot for 2s, both sides / Details: Vitrification instrument: Cryoplunge CP3 gatan

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Details: Images recorded on a JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 45591 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2500 nm / Energy filter: Omega JEOL / Energy window: 0-20 eV
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC / Temperature: 98.15 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 100 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 10 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 15171 / Applied symmetry: D3 (2*3 fold dihedral)
3D reconstructionAlgorithm: Projection matching / Software: IMAGIC / CTF correction: Each particle / Resolution: 26 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: The initial fit was done by manual docking followed by refinement using the (fit in map) Chimera plugging
Input PDB model: 2X8K

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