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- EMDB-6560: Bacteriophage phi29 prohead particle stalled during DNA packaging -

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Basic information

Entry
Database: EMDB / ID: EMD-6560
TitleBacteriophage phi29 prohead particle stalled during DNA packaging
Map dataReconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP
Sample
  • Sample: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction.
  • Virus: Bacillus phage phi29 (virus)
Keywordsbacteriophage phi29 / ATPase / DNA packaging motor
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsMao H / Saha M / Reyes-Aldrete E / Sherman M / Woodson M / Jardine PJ / Grimes S / Morais M
CitationJournal: Cell Rep / Year: 2016
Title: Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.
Authors: Huzhang Mao / Mitul Saha / Emilio Reyes-Aldrete / Michael B Sherman / Michael Woodson / Rockney Atz / Shelley Grimes / Paul J Jardine / Marc C Morais /
Abstract: Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline ...Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.
History
DepositionDec 20, 2015-
Header (metadata) releaseMar 9, 2016-
Map releaseMar 9, 2016-
UpdateApr 27, 2016-
Current statusApr 27, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6560.gif

Downloads & links

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Map

FileDownload / File: emd_6560.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 400 pix.
= 776. Å		1.94 Å/pix.
x 400 pix.
= 776. Å		1.94 Å/pix.
x 400 pix.
= 776. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.92879784 - 4.93663359
Average (Standard dev.)0.11919545 (±0.4228709)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 776.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.941.941.94
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z776.000776.000776.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.9294.9370.119

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Supplemental data

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Sample components

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Entire : Reconstruction of bacteriophage phi29 stalled during DNA packagin...

EntireName: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction.
Components
  • Sample: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction.
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1000: Reconstruction of bacteriophage phi29 stalled during DNA packagin...

SupramoleculeName: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction.
type: sample / ID: 1000
Oligomeric state: The particle is based on a prolate icosahedron with T = 3, Q = 5 quasi-symmetry wherein one pentameric capsomer at one end of the particle is replaced by a dodecameric gp10 ...Oligomeric state: The particle is based on a prolate icosahedron with T = 3, Q = 5 quasi-symmetry wherein one pentameric capsomer at one end of the particle is replaced by a dodecameric gp10 connector protein and a pentameric pRNA and gp16 ATPase ring.
Number unique components: 1

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Name.synonym: bacteriophage phi29
Details: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. After two minutes incubation, DNAses were added to remove unpackaged DNA. Only particles ...Details: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. After two minutes incubation, DNAses were added to remove unpackaged DNA. Only particles that had clearly packaged were included in the reconstruction.
NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: bacteriophage phi29
Host (natural)Organism: Bacillus subtilis (bacteria) / 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: 7.8 / Details: 25 mM Tris-HCl, 5 mM MgCl2, 50 mM NaCl
GridDetails: Quantifoil holey carbon on top of 200 mesh copper grid, plasma-cleaned
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: Blot from behind the sample for 4 seconds before plunging.

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Electron microscopy

MicroscopeJEOL 2200FS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
Specialist opticsEnergy filter - Name: JEOL
DateJun 24, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using semi-automatic particle selection, followed by manual deletion of bad particles and manual selection of missed particles.
CTF correctionDetails: Each Micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: EMAN
Details: C5 symmetry was imposed in all stages of the reconstruction, with the 5-fold axis along Z. The final map was low-pass filtered at 14 Angstrom.
Number images used: 1871

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