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- EMDB-3394: Cryo-electron microscopy structure of the hexagonal pre-attachmen... -

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Basic information

Entry
Database: EMDB / ID: EMD-3394
TitleCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the upper peripheral baseplate
Map dataCryo-electron microscopy structure of the upper peripheral baseplate region of the hexagonal pre-attachment T4 baseplate-tail tube complex. Post-processed with RELION.The map is slightly offset with respect to the complete reconstruction of the hexagonal pre-attachment baseplate.
Sample
  • Sample: Hexagonal pre-attachment T4 baseplate-tail tube complex
  • Protein or peptide: Hexagonal pre-attachment T4 baseplate-tail tube complex
KeywordsT4 / baseplate-tail tube complex / pre-attachment / bacteriophage / bacterial virus / hexagonal / membrane-piercing / cell attachment / infection
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.55 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: 0.0296
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0296
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3394.png

Downloads & links

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Map

FileDownload / File: emd_3394.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy structure of the upper peripheral baseplate region of the hexagonal pre-attachment T4 baseplate-tail tube complex. Post-processed with RELION.The map is slightly offset with respect to the complete reconstruction of the hexagonal pre-attachment baseplate.
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: 0.0296 / Movie #1: 0.0296
Minimum - Maximum-0.02709264 - 0.08065169
Average (Standard dev.)0.00011014 (±0.00184489)
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-0.0270.0810.000

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Supplemental data

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Sample components

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Entire : Hexagonal pre-attachment T4 baseplate-tail tube complex

EntireName: Hexagonal pre-attachment T4 baseplate-tail tube complex
Components
  • Sample: Hexagonal pre-attachment T4 baseplate-tail tube complex
  • Protein or peptide: Hexagonal pre-attachment T4 baseplate-tail tube complex

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Supramolecule #1000: Hexagonal pre-attachment T4 baseplate-tail tube complex

SupramoleculeName: Hexagonal pre-attachment T4 baseplate-tail tube complex
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 localized reconstruction of the upper peripheral baseplate region of the hexagonal pre-attachment baseplate-tail tube complex.
Oligomeric state: (gp3)6(gp5)3(gp5.4)1(gp6)12(gp7)6(gp8)12(gp9)18(gp10)18(gp11)18(gp12)18(gp19)126(gp25)6(gp27)3(gp29)X(gp48)6(gp53)6(gp54)6
Number unique components: 1
Molecular weightTheoretical: 8.7 MDa

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Macromolecule #1: Hexagonal pre-attachment T4 baseplate-tail tube complex

MacromoleculeName: Hexagonal pre-attachment T4 baseplate-tail tube complex
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: 4.55 Å / Resolution method: OTHER / Software - Name: RELION
Details: Only the baseplate and the proximal part of the tail tube were selected for 3D reconstruction. The total mass of the reconstructed volume was approximately 6.5 MDa. Then, we performed ...Details: Only the baseplate and the proximal part of the tail tube were selected for 3D reconstruction. The total mass of the reconstructed volume was approximately 6.5 MDa. Then, we performed locally masked refinement of the upper peripheral baseplate region.
Number images used: 37913
FSC plot (resolution estimation)

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