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- EMDB-3396: Cryo-electron microscopy structure of the star-shaped, hubless po... -

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Basic information

Entry
Database: EMDB / ID: EMD-3396
TitleCryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate
Map dataCryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate. Postprocessed with Relion, using automated B-factor estimation and the mask used for polishing, which was generated previously by auto-masking with an initial binarization threshold of 0.015.
Sample
  • Sample: Star-shaped, hubless post-attachment T4 baseplate
  • Protein or peptide: Star-shaped, hubless post-attachment T4 baseplate
KeywordsT4 / baseplate / post-attachment / bacteriophage / bacterial virus / star-shaped / hubless / membrane-piercing / cell attachment / infection
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell / identical protein binding
Similarity search - Function
Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Baseplate structural protein Gp11 ...Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / 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 / 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 / IraD/Gp25-like / Baseplate wedge protein gp25 / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Baseplate wedge protein gp53 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.77 Å
AuthorsTaylor NMI / Guerrero-Ferreira RC / Goldie KN / Stahlberg H / Leiman PG
CitationJournal: Nature / Year: 2016
Title: Structure of the T4 baseplate and its function in triggering sheath contraction.
Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /
Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This macromolecular machine resembles a stretched, coiled spring (or sheath) wound around a rigid tube with a spike-shaped protein at its tip. A baseplate structure, which is arguably the most complex part of this assembly, relays the contraction signal to the sheath. Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. We establish the identity and function of a minimal set of components that is conserved in all contractile injection systems and show that the triggering mechanism is universally conserved.
History
DepositionMar 17, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseMay 18, 2016-
UpdateMay 18, 2016-
Current statusMay 18, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5iv7
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3396.png

Downloads & links

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Map

FileDownload / File: emd_3396.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy structure of the star-shaped, hubless post-attachment T4 baseplate. Postprocessed with Relion, using automated B-factor estimation and the mask used for polishing, which was generated previously by auto-masking with an initial binarization threshold of 0.015.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 480 pix.
= 636.48 Å		1.33 Å/pix.
x 480 pix.
= 636.48 Å		1.33 Å/pix.
x 480 pix.
= 636.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.326 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0095 / Movie #1: 0.0095
Minimum - Maximum-0.00931757 - 0.03741582
Average (Standard dev.)0.00031558 (±0.00200508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 636.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3261.3261.326
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z636.480636.480636.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0090.0370.000

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Supplemental data

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Sample components

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Entire : Star-shaped, hubless post-attachment T4 baseplate

EntireName: Star-shaped, hubless post-attachment T4 baseplate
Components
  • Sample: Star-shaped, hubless post-attachment T4 baseplate
  • Protein or peptide: Star-shaped, hubless post-attachment T4 baseplate

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Supramolecule #1000: Star-shaped, hubless post-attachment T4 baseplate

SupramoleculeName: Star-shaped, hubless post-attachment T4 baseplate / type: sample / ID: 1000
Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current reconstruction is the ...Details: In addition to hexagonal pre-attachment baseplate-tail tube complexes, the sample also contained some star-shaped, hubless post-attachment baseplates. The current reconstruction is the reconstruction of those post-attachment, star-shaped baseplates, which have the following oligomeric state: (gp6)12(gp7)6(gp8)12(gp9)18(gp10)18(gp11)18(gp12)18(gp25)6(gp53)6. This oligomeric state has an approximate theoretical MW of 5.5 MDa.
Oligomeric state: (gp6)12(gp7)6(gp8)12(gp9)18(gp10)18(gp11)18(gp12)18(gp25)6(gp53)6
Number unique components: 1
Molecular weightTheoretical: 5.5 MDa

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Macromolecule #1: Star-shaped, hubless post-attachment T4 baseplate

MacromoleculeName: Star-shaped, hubless post-attachment T4 baseplate / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Enterobacteria phage T4 (virus) / Strain: am18/am23 mutant
Molecular weightTheoretical: 8.7 MDa

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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

Concentration1 mg/mL
BufferpH: 8 / Details: 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 8 mM MgSO4
GridDetails: Quantifoil 300 mesh carbon-coated copper grids glow-discharged for 20 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: Applied 3.5 ul of sample and blotting 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: The astigmatism was corrected at high magnification
Specialist opticsEnergy filter - Name: Quantum-LS Gatan Image Filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateMay 7, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1621 / Average electron dose: 60 e/Å2
Details: Individual frames were aligned with 2dx_automator. 40 frames were recorded in total, and the 2 first frames were discarded.
Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected with e2boxer.py.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.77 Å / Resolution method: OTHER / Software - Name: RELION
Details: The short tail fibers (gp12 trimers) appear more flexible, and no special effort was made to reconstruct them. They were partly masked out by the circular mask.The total mass of the ...Details: The short tail fibers (gp12 trimers) appear more flexible, and no special effort was made to reconstruct them. They were partly masked out by the circular mask.The total mass of the reconstructed volume was approximately 4.5 MDa.
Number images used: 5176
FSC plot (resolution estimation)

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