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- EMDB-3374: Cryo-electron microscopy structure of the hexagonal pre-attachmen... -

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Basic information

Entry
Database: EMDB / ID: EMD-3374
TitleCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex
Map dataCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex. Post-processed with RELION, using auto-masking with initial binarization threshold of 0.011.
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
Function / homology
Function and homology information


peptidoglycan beta-N-acetylmuramidase activity / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / virus tail ...peptidoglycan beta-N-acetylmuramidase activity / symbiont genome ejection through host cell envelope, contractile tail mechanism / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, tube / virus tail, baseplate / virus tail, fiber / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / virus tail / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / structural molecule activity / identical protein binding / metal ion binding
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp12 / Baseplate wedge protein gp53, bacteriophage T4 / Short tail fibre protein, C-terminal / Baseplate wedge protein gp7 / Short tail fibre protein, C-terminal superfamily / : / : / : ...Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp12 / Baseplate wedge protein gp53, bacteriophage T4 / Short tail fibre protein, C-terminal / Baseplate wedge protein gp7 / Short tail fibre protein, C-terminal superfamily / : / : / : / Phage short tail fibre protein gp12, middle domain / Base plate wedge protein 53 / Short tail fibre protein receptor-binding domain / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Phage tail collar domain / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Phage tail collar domain superfamily / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Phage Tail Collar Domain / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / 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 / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / PAAR motif / PAAR motif / IraD/Gp25-like / Baseplate wedge protein gp25 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold
Similarity search - Domain/homology
Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Short tail fiber protein gp12 / Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54 / Pre-baseplate central spike protein Gp5 / Baseplate wedge protein gp53 ...Baseplate wedge protein gp25 / Baseplate protein gp9 / Baseplate wedge protein gp10 / Baseplate wedge protein gp11 / Short tail fiber protein gp12 / Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54 / Pre-baseplate central spike protein Gp5 / Baseplate wedge protein gp53 / Baseplate central spike complex protein gp27 / Baseplate wedge protein gp6 / Baseplate wedge protein gp7 / Baseplate wedge protein gp8 / Baseplate puncturing device gp5.4
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.11 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 9, 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: 0.0263
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0263
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5iv5
  • Surface level: 0.0263
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3374.png

Downloads & links

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Map

FileDownload / File: emd_3374.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex. Post-processed with RELION, using auto-masking with initial binarization threshold of 0.011.
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: 0.0263 / Movie #1: 0.0263
Minimum - Maximum-0.08156577 - 0.13545899
Average (Standard dev.)0.00073391 (±0.00481781)
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-0.0820.1350.001

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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 overall reconstruction 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: 4.11 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.
Number images used: 37913
FSC plot (resolution estimation)

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