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- EMDB-3395: Cryo-electron microscopy structure of the hexagonal pre-attachmen... -

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Basic information

Entry
Database: EMDB / ID: 3395
TitleCryo-electron microscopy structure of the hexagonal pre-attachment T4 baseplate-tail tube complex: locally masked refinement of the lower peripheral baseplate
Map dataCryo-electron microscopy structure of the lower 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.
SampleHexagonal pre-attachment T4 baseplate-tail tube complex:
KeywordsT4 / baseplate-tail tube complex / pre-attachment / bacteriophage / bacterial virus / hexagonal / membrane-piercing / cell attachment / infection
SourceEnterobacteria phage T4 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / 4.45 Å resolution
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
DateDeposition: Mar 17, 2016 / Header (metadata) release: Apr 13, 2016 / Map release: May 18, 2016 / Last update: May 18, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0252
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3395.map.gz (map file in CCP4 format, 432001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.33 Å/pix.
= 636.48 Å
480 pix
1.33 Å/pix.
= 636.48 Å
480 pix
1.33 Å/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
Contour Level:0.0252 (by author), 0.0252 (movie #1):
Minimum - Maximum-0.02216877 - 0.08436013
Average (Standard dev.)0.00025608 (0.00250418)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 636.48 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0220.0840.000

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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
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 lower peripheral baseplate region of the hexagonal pre-attachment baseplate-tail tube complex.
Number of components: 1
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
MassTheoretical: 8.7 MDa

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Component #1: protein, Hexagonal pre-attachment T4 baseplate-tail tube complex

ProteinName: Hexagonal pre-attachment T4 baseplate-tail tube complex
Recombinant expression: No / Number of Copies: 1
MassTheoretical: 8.7 MDa
SourceSpecies: Enterobacteria phage T4 (bacteriophage) / Strain: am18/am23 mutant

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 50 mM Tris-HCl pH 8.0, 100 mM NaCl, 8 mM MgSO4
pH: 8
Support filmQuantifoil 300 mesh carbon-coated copper grids glow-discharged for 20 seconds
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Method: Applied 3.5 ul of sample and blotting 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: May 7, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal), 37700 X (calibrated)
Astigmatism: The astigmatism was corrected at high magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4000 nm / Energy filter: Quantum-LS Gatan Image Filter / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1621 / Bit depth: 32
Details: Individual frames were aligned with 2dx_automator. 40 frames were recorded in total, and the 2 first frames were discarded.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 37913 / Details: The particles were selected with e2boxer.py.
3D reconstructionAlgorithm: Single particle reconstruction / Software: RELION / CTF correction: Each particle
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 lower peripheral baseplate region.
Resolution: 4.45 Å / Resolution method: FSC 0.143, gold-standard
FSC plot
(resolution estimation)

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