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- EMDB-1573: The bacteriophage T4 procapsid in the process of DNA packaging -

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Basic information

Entry
Database: EMDB / ID: EMD-1573
TitleThe bacteriophage T4 procapsid in the process of DNA packaging
Map dataThe bacteriophage T4 procapsid in the process of DNA packaging
Sample
  • Sample: T4 procapsid in the process of DNA packaging
  • Virus: Enterobacteria phage T4 (virus)
Keywordsprocapsid / DNA packaging motor / large terminase
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 32.0 Å
AuthorsSun S / Kondabagil K / Draper B / Alam TI / Bowman VD / Zhang Z / Hegde S / Fokine A / Rossmann MG / Rao VB
CitationJournal: Cell / Year: 2008
Title: The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.
Authors: Siyang Sun / Kiran Kondabagil / Bonnie Draper / Tanfis I Alam / Valorie D Bowman / Zhihong Zhang / Shylaja Hegde / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The ...Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.
History
DepositionOct 23, 2008-
Header (metadata) releaseOct 23, 2008-
Map releaseMay 5, 2009-
UpdateMay 5, 2009-
Current statusMay 5, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1573.gif

Downloads & links

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Map

FileDownload / File: emd_1573.map.gz / Format: CCP4 / Size: 54.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe bacteriophage T4 procapsid in the process of DNA packaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.48 Å/pix.
x 244 pix.
= 1581.12 Å		6.48 Å/pix.
x 244 pix.
= 1581.12 Å		6.48 Å/pix.
x 244 pix.
= 1581.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.5
Minimum - Maximum-6.80765 - 10.076499999999999
Average (Standard dev.)-0.00000000305768 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-122-122-122
Dimensions244244244
Spacing244244244
CellA=B=C: 1581.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.486.486.48
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z1581.1201581.1201581.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-122-122-122
NC/NR/NS244244244
D min/max/mean-6.80810.076-0.000

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Supplemental data

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Sample components

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Entire : T4 procapsid in the process of DNA packaging

EntireName: T4 procapsid in the process of DNA packaging
Components
  • Sample: T4 procapsid in the process of DNA packaging
  • Virus: Enterobacteria phage T4 (virus)

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Supramolecule #1000: T4 procapsid in the process of DNA packaging

SupramoleculeName: T4 procapsid in the process of DNA packaging / type: sample / ID: 1000 / Details: T4 procapsids with gp17, 4Kb DNA and ATP / Number unique components: 4

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Supramolecule #1: Enterobacteria phage T4

SupramoleculeName: Enterobacteria phage T4 / type: virus / ID: 1 / Name.synonym: bacteriophage T4 / NCBI-ID: 10665 / Sci species name: Enterobacteria phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage T4
Host (natural)Organism: E. Coli (E. coli) / synonym: BACTERIA(EUBACTERIA)

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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

BufferpH: 7.4
Details: 50mM Tris-HCl, 100mM NaCl, 5mM MgCl2, 3mM beta-mercaptoethanol
GridDetails: quantifoil copper grid 2um holes
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: in-house, gravity driven plunger
Method: 3.5ul of sample hand blotted approx. 1sec

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 97 K
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: 100 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: phase flipping for each micrograph
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 2001

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