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- EMDB-6323: CryoEM single particle reconstruction of prolate head of bacterio... -

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Basic information

Entry
Database: EMDB / ID: EMD-6323
TitleCryoEM single particle reconstruction of prolate head of bacteriophage T4
Map dataReconstruction of empty T4 prolate head
Sample
  • Sample: empty T4 prolate head
  • Virus: Enterobacteria phage T4 (virus)
KeywordsT4 prolate head
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsSun L / Zhang X / Gao S / Rao PA / Padilla-Sanchez V / Chen Z / Sun S / Xiang Y / Rao VB / Rossmann MG
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.
Authors: Lei Sun / Xinzheng Zhang / Song Gao / Prashant A Rao / Victor Padilla-Sanchez / Zhenguo Chen / Siyang Sun / Ye Xiang / Sriram Subramaniam / Venigalla B Rao / Michael G Rossmann /
Abstract: The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage ...The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.
History
DepositionApr 21, 2015-
Header (metadata) releaseMay 6, 2015-
Map releaseJul 22, 2015-
UpdateJul 22, 2015-
Current statusJul 22, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6323.gif

Downloads & links

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Map

FileDownload / File: emd_6323.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of empty T4 prolate head
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 640 pix.
= 1408. Å		2.2 Å/pix.
x 640 pix.
= 1408. Å		2.2 Å/pix.
x 640 pix.
= 1408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55 / Movie #1: 0.55
Minimum - Maximum-1.30446398 - 10.446558
Average (Standard dev.)0.11265536 (±0.60943025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z1408.0001408.0001408.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-1.30410.4470.113

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Supplemental data

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Sample components

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Entire : empty T4 prolate head

EntireName: empty T4 prolate head
Components
  • Sample: empty T4 prolate head
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: empty T4 prolate head

SupramoleculeName: empty T4 prolate head / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 82 MDa

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Details: empty head / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Molecular weightTheoretical: 82 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: 7.5 / Details: 50 mM Tris, 1 mM MgCl2, 100 mM NaCl
GridDetails: 400 mesh copper grid with thin holey carbon film, glow discharged in amylamine atmosphere
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification.
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
DateAug 9, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 473 / Average electron dose: 22.0 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60521 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Liquid nitrogen-cooled / Specimen 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 using an automatic selection program.
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 13000

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