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- EMDB-1082: The PM2 virion has a novel organization with an internal membrane... -

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Basic information

Entry
Database: EMDB / ID: EMD-1082
TitleThe PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes.
Map dataThis is the PM2 virion reconstruction
Sample
  • Sample: PM2 virion
  • Virus: Pseudoalteromonas phage PM2 (virus)
Biological speciesPseudoalteromonas phage PM2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsHuiskonen JT / Kivela HM / Bamford DH / Butcher SJ
CitationJournal: Nat Struct Mol Biol / Year: 2004
Title: The PM2 virion has a novel organization with an internal membrane and pentameric receptor binding spikes.
Authors: Juha T Huiskonen / Hanna M Kivelä / Dennis H Bamford / Sarah J Butcher /
Abstract: Biological membranes are notoriously resistant to structural analysis. Excellent candidates to tackle this problem in situ are membrane-containing viruses where the membrane is constrained by an ...Biological membranes are notoriously resistant to structural analysis. Excellent candidates to tackle this problem in situ are membrane-containing viruses where the membrane is constrained by an icosahedral capsid. Cryo-EM and image reconstruction of bacteriophage PM2 revealed a membrane bilayer following the internal surface of the capsid. The viral genome closely interacts with the inner leaflet. The capsid, at a resolution of 8.4 A, reveals 200 trimeric capsomers with a pseudo T = 21 dextro organization. Pentameric receptor-binding spikes protrude from the surface. It is evident from the structure that the PM2 membrane has at least two important roles in the life cycle. First, it acts as a scaffold to nucleate capsid assembly. Second, after host recognition, it fuses with the host outer membrane to promote genome entry. The structure also sheds light on how the viral supercoiled circular double-stranded DNA genome might be packaged and released.
History
DepositionMay 17, 2004-
Header (metadata) releaseMay 25, 2004-
Map releaseMay 25, 2005-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 400
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 400
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1082.gif

Downloads & links

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Map

FileDownload / File: emd_1082.map.gz / Format: CCP4 / Size: 392.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThis is the PM2 virion reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 595 pix.
= 861. Å		1.4 Å/pix.
x 595 pix.
= 861. Å		1.4 Å/pix.
x 595 pix.
= 861. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1460.0 / Movie #1: 400
Minimum - Maximum-2340.0 - 3865.0
Average (Standard dev.)0.437353 (±679.682999999999993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions595595595
Spacing595595595
CellA=B=C: 861 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.41.41.4
M x/y/z615615615
origin x/y/z0.0000.0000.000
length x/y/z861.000861.000861.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-20-59
NX/NY/NZ181231119
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS595595595
D min/max/mean-2340.0003865.0000.437

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Supplemental data

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Sample components

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Entire : PM2 virion

EntireName: PM2 virion
Components
  • Sample: PM2 virion
  • Virus: Pseudoalteromonas phage PM2 (virus)

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Supramolecule #1000: PM2 virion

SupramoleculeName: PM2 virion / type: sample / ID: 1000
Details: Purified virion (1 mg/ml) was purified, pelleted and resuspended just prior to application to the grid.
Number unique components: 1
Molecular weightTheoretical: 33.8 MDa
Method: Reported mass of the whole virion in the literature is 47 MDa, 72 percent of which is protein.

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Supramolecule #1: Pseudoalteromonas phage PM2

SupramoleculeName: Pseudoalteromonas phage PM2 / type: virus / ID: 1 / Name.synonym: PM2 / Details: includes mass of DNA, lipid and protein / NCBI-ID: 10661 / Sci species name: Pseudoalteromonas phage PM2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: PM2
Host (natural)Organism: Pseudoalteromonas sp. ER72M2 (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 47 MDa
Virus shellShell ID: 1 / Name: P2 / Diameter: 597 Å / T number (triangulation number): 21
Virus shellShell ID: 2 / Name: virion (spike-spike distance) / Diameter: 765 Å / T number (triangulation number): 21

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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

Concentration4 mg/mL
BufferpH: 7.2 / Details: CaCl2, 5mM Tris-HCl, 10-20 mM NaCl, 25-125 mM
GridDetails: 400 mesh copper grid, R2/2 quantifoil holey
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 94 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
DetailsA box anticontaminator was fitted with a minimum achievable temperature of 88 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 111 / Average electron dose: 10 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were first automatically selected using ETHAN, and then boxed out manually in EMAN.
CTF correctionDetails: each particle, wiener factor 0.1
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMBL, P3DR / Number images used: 13887

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