EMDB-1086: Three-dimensional rearrangement of proteins in the tail of bacter...

Basic information

• Entry: Database: EMDB / ID: EMD-1086
• Title: Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.
• Map data: CryoEM density of the T4 tail with contracted sheath and the baseplate in the star conformation.

Sample

• Sample: T4 phages treated with 3 M urea
• Virus: Enterobacteria phage T4 (virus)

Function / homology

Function:

virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, baseplate / viral tail assembly / viral release from host cell / virion component / identical protein binding

Domain/homology:

Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / : / GP11 baseplate wedge protein / Tail sheath protein Gp18-like domain I / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain

Component:

Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Tail completion protein gp15 / Tail sheath protein / Baseplate wedge protein gp6 / Baseplate wedge protein gp8

• Biological species: Enterobacteria phage T4 (virus)
• Method: single particle reconstruction / cryo EM / Resolution: 16.0 Å
• Authors: Leiman PG / Chipman PR / Kostyuchenko VA / Mesyanzhinov VV / Rossmann MG
• Citation: Journal: Cell / Year: 2004; Title: Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.; Authors: Petr G Leiman / Paul R Chipman / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann / ; Abstract: The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal to a star shape. This causes the sheath around the tail tube to contract and the tail tube to protrude from the baseplate and pierce the outer cell membrane and the cell wall before reaching the inner cell membrane for subsequent viral DNA injection. Analogously, the T4 tail can be contracted by treatment with 3 M urea. The structure of the T4 contracted tail, including the head-tail joining region, has been determined by cryo-electron microscopy to 17 A resolution. This 1200 A-long, 20 MDa structure has been interpreted in terms of multiple copies of its approximately 20 component proteins. A comparison with the metastable hexagonal baseplate of the mature virus shows that the baseplate proteins move as rigid bodies relative to each other during the structural change.

History

Deposition	Jun 3, 2004	-
Header (metadata) release	Jun 3, 2004	-
Map release	Sep 7, 2004	-
Update	Apr 17, 2013	-
Current status	Apr 17, 2013	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_1086.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: CryoEM density of the T4 tail with contracted sheath and the baseplate in the star conformation.
• Voxel size: X=Y=Z: 3.93285 Å

Density

Contour Level	By AUTHOR: 1.5 / Movie #1: 2.2
Minimum - Maximum	-11.223052020000001 - 14.634929659999999
Average (Standard dev.)	0.0 (±1.0)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -128 -128 -127 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 1006.8096 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	3.9328515625	3.9328515625	3.9328515625
M x/y/z	256	256	256
origin x/y/z	0.000	0.000	0.000
length x/y/z	1006.810	1006.810	1006.810
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	-30	-20	-59
NX/NY/NZ	181	231	119
MAP C/R/S	1	2	3
start NC/NR/NS	-128	-128	-127
NC/NR/NS	256	256	256
D min/max/mean	-11.223	14.635	0.000

Supplemental data

Sample components

Entire : T4 phages treated with 3 M urea

• Entire: Name: T4 phages treated with 3 M urea

Components

• Sample: T4 phages treated with 3 M urea
• Virus: Enterobacteria phage T4 (virus)

Supramolecule #1000: T4 phages treated with 3 M urea

• Supramolecule: Name: T4 phages treated with 3 M urea / type: sample / ID: 1000 / Number unique components: 1
• Molecular weight: Experimental: 220 MDa / Theoretical: 220 MDa / Method: Estimate

Supramolecule #1: Enterobacteria phage T4

• Supramolecule: Name: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: phage T4 / Details: treated with 3 M urea / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: phage T4
• Host (natural): Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
• Molecular weight: Experimental: 220 MDa / Theoretical: 220 MDa

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 5 mg/mL
• Buffer: pH: 7.5 / Details: H2O
• Grid: Details: 200 mesh cupper grid
• Vitrification: Cryogen name: ETHANE / Chamber temperature: 100 K

Electron microscopy

• Microscope: FEI/PHILIPS CM300FEG/T
• Temperature: Average: 100 K
• Specialist optics: Energy filter - Name: FEI
• Date: Jan 6, 2002
• Image recording: Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 3.93285 µm / Number real images: 100 / Average electron dose: 20 e/Ų / Bits/pixel: 8
• Tilt angle min: 0
• Tilt angle max: 0
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Calibrated magnification: 47000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
• Sample stage: Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder; Specimen holder model: GATAN LIQUID NITROGEN

Image processing

• CTF correction: Details: Each particle
• Final reconstruction: Applied symmetry - Point group: C₆ (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 1965
• Final angle assignment: Details: theta 45 degrees, phi 180 degrees

Atomic model buiding 1

Initial model

PDB ID:

1n7z

• Software: Name: Situs v.2.0
• Details: The components were separately fitted using Situs v.2.0
• Refinement: Space: REAL

Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

PDB-3foi:
Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 contracted tail

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail

Atomic model buiding 2

Initial model

PDB ID:

1s2e

• Software: Name: Situs v.2.0
• Details: The components were separately fitted using Situs v.2.0
• Refinement: Space: REAL

Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

PDB-3foi:
Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 contracted tail

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail

Atomic model buiding 3

Initial model

PDB ID:

1el6

• Software: Name: Situs v.2.0
• Details: The components were separately fitted using Situs v.2.0
• Refinement: Space: REAL

Output model

PDB-1tja:
Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail

PDB-2fl9:
Evolution of bacteriophage tails: Structure of T4 gene product 10

PDB-3foi:
Fitting of gp18M crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 contracted tail

PDB-3h3y:
Fitting of the gp6 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 star-shaped baseplate

PDB-3j2n:
The X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the contracted T4 tail