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- EMDB-1119: Three-dimensional structure of the bacteriophage P22 tail machine. -

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Basic information

Entry
Database: EMDB / ID: EMD-1119
TitleThree-dimensional structure of the bacteriophage P22 tail machine.
Map dataa cryoEM map of the P22 tail machine
Sample
  • Sample: the tail machine isolated from bacteriophage P22
  • Protein or peptide: portal
  • Protein or peptide: tailspike
  • Protein or peptide: gp4
  • Protein or peptide: gp10
  • Protein or peptide: gp26
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsTang L / Marion WR / Cingolani G / Prevelige PE / Johnson JE
CitationJournal: EMBO J / Year: 2005
Title: Three-dimensional structure of the bacteriophage P22 tail machine.
Authors: Liang Tang / William R Marion / Gino Cingolani / Peter E Prevelige / John E Johnson /
Abstract: The tail of the bacteriophage P22 is composed of multiple protein components and integrates various biological functions that are crucial to the assembly and infection of the phage. The three- ...The tail of the bacteriophage P22 is composed of multiple protein components and integrates various biological functions that are crucial to the assembly and infection of the phage. The three-dimensional structure of the P22 tail machine determined by electron cryo-microscopy and image reconstruction reveals how the five types of polypeptides present as 51 subunits are organized into this molecular machine through twelve-, six- and three-fold symmetry, and provides insights into molecular events during host cell attachment and phage DNA translocation.
History
DepositionApr 1, 2005-
Header (metadata) releaseApr 4, 2005-
Map releaseJun 20, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.275232
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.275232
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1119.gif

Downloads & links

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Map

FileDownload / File: emd_1119.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationa cryoEM map of the P22 tail machine
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 160 pix.
= 672. Å		4.2 Å/pix.
x 160 pix.
= 672. Å		4.2 Å/pix.
x 160 pix.
= 672. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.326 / Movie #1: 1.275232
Minimum - Maximum-6.90755 - 6.64187
Average (Standard dev.)-0.0198402 (±0.345698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-79-79-79
Dimensions160160160
Spacing160160160
CellA=B=C: 672 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z672.000672.000672.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-80-80-80
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-79-79-79
NC/NR/NS160160160
D min/max/mean-6.9086.642-0.020

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Supplemental data

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Sample components

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Entire : the tail machine isolated from bacteriophage P22

EntireName: the tail machine isolated from bacteriophage P22
Components
  • Sample: the tail machine isolated from bacteriophage P22
  • Protein or peptide: portal
  • Protein or peptide: tailspike
  • Protein or peptide: gp4
  • Protein or peptide: gp10
  • Protein or peptide: gp26

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Supramolecule #1000: the tail machine isolated from bacteriophage P22

SupramoleculeName: the tail machine isolated from bacteriophage P22 / type: sample / ID: 1000 / Oligomeric state: 12-, 6-, and 3-fold symmetry / Number unique components: 5
Molecular weightTheoretical: 2.8 MDa

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Macromolecule #1: portal

MacromoleculeName: portal / type: protein_or_peptide / ID: 1 / Name.synonym: gp1 / Details: DNA packaging / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101
Molecular weightExperimental: 82.611 MDa / Theoretical: 83 MDa
Recombinant expressionOrganism: Salmonella enterica Serovar Typhimurium strain

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Macromolecule #2: tailspike

MacromoleculeName: tailspike / type: protein_or_peptide / ID: 2 / Name.synonym: gp9 / Details: receptor binding / Number of copies: 18 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101
Molecular weightExperimental: 71.857 MDa / Theoretical: 70 MDa
Recombinant expressionOrganism: Salmonella enterica Serovar Typhimurium strain

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Macromolecule #3: gp4

MacromoleculeName: gp4 / type: protein_or_peptide / ID: 3 / Name.synonym: accessory protein / Details: forms a channel; transglycosylase / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101
Molecular weightExperimental: 18.025 MDa / Theoretical: 20 MDa
Recombinant expressionOrganism: Salmonella enterica Serovar Typhimurium strain

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Macromolecule #4: gp10

MacromoleculeName: gp10 / type: protein_or_peptide / ID: 4 / Name.synonym: accessory protein / Details: forms a channel / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101
Molecular weightExperimental: 52.457 MDa / Theoretical: 50 MDa
Recombinant expressionOrganism: Salmonella enterica Serovar Typhimurium strain

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Macromolecule #5: gp26

MacromoleculeName: gp26 / type: protein_or_peptide / ID: 5 / Name.synonym: accessory protein / Details: needle-like plug / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage P22 (virus) / Strain: 13-am H101
Molecular weightExperimental: 24.603 MDa / Theoretical: 25 MDa
Recombinant expressionOrganism: Salmonella enterica Serovar Typhimurium strain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 50 mM Na2HPO4, pH8.0
GridDetails: 300 mesh holey copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made plunger / Method: blot for 3-4 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 89 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 105,000 times magnification
DateMay 19, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 54 / Bits/pixel: 8
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 60

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Image processing

DetailsThe particles showed preferential orientation on the grids. CryoEM data were collected using the tilt method. The tilt angles ranged from 0-60 degrees. The particles were selected with a semi-automated selection program.
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 11329
Final angle assignmentDetails: SPIDER:theta 90 degrees, phi 60 degrees

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Atomic model buiding 1

Initial model(PDB ID:

1tyx

,

1lkt

)
SoftwareName: colores
DetailsProtocol: rigid body. The receptor-binding domain (1TYX) of the tailspike was computationally docked with the program colores, and the docking was unambiguous. Then the head-binding domain (1LKT) was manually docked.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient

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