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- EMDB-2413: cryo-electron tomography of poliovirus-PVR-liposome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2413
Titlecryo-electron tomography of poliovirus-PVR-liposome complex
Map dataSubtomogram asymmetric average of 206 selected virus particles attached to membrane.
Sample
  • Sample: selected "best" average 135S poliovirus - membrane complex
  • Virus: Human poliovirus 1 Mahoney
Keywordspoliovirus PVR poliovirus receptor liposome 135S
Biological speciesHuman poliovirus 1 Mahoney
Methodsubtomogram averaging / cryo EM
AuthorsStrauss M / Levy HC / Bostina M / Filman DJ / Hogle JM
CitationJournal: J Virol / Year: 2013
Title: RNA transfer from poliovirus 135S particles across membranes is mediated by long umbilical connectors.
Authors: Mike Strauss / Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle /
Abstract: During infection, the binding of poliovirus to its cell surface receptor at 37°C triggers an expansion of the virus in which internal polypeptides that bind to membranes are externalized. ...During infection, the binding of poliovirus to its cell surface receptor at 37°C triggers an expansion of the virus in which internal polypeptides that bind to membranes are externalized. Subsequently, in a poorly understood process, the viral RNA genome is transferred directly across an endosomal membrane, and into the host cell cytoplasm, to initiate infection. Here, cryoelectron tomography demonstrates the results of 37°C warming of a poliovirus-receptor-liposome model complex that was produced using Ni-nitrilotriacetic acid lipids and His-tagged receptor ectodomains. In total, 651 subtomographic volumes were aligned, classified, and averaged to obtain detailed pictures, showing both the conversion of virus into its expanded form and the passage of RNA into intact liposomes. Unexpectedly, the virus and membrane surfaces were located ∼50 Å apart, with the 5-fold axis tilted away from the perpendicular, and the solvent spaces between them were spanned by either one or two long "umbilical" density features that lie at an angle to the virus and membrane. The thinner connector, which sometimes appears alone, is 28 to 30 Å in diameter and has a footprint on the virus surface located close to either a 5-fold or a 3-fold axis. The broader connector has a footprint near the quasi-3-fold hole that opens upon virus expansion and is hypothesized to include RNA, shielded from enzymatic degradation by polypeptides that include the N-terminal extension of VP1 and capsid protein VP4. The implications of these observations for the mechanism of RNase-protected RNA transfer in picornaviruses are discussed.
History
DepositionJul 5, 2013-
Header (metadata) releaseJul 17, 2013-
Map releaseJul 17, 2013-
UpdateJul 24, 2013-
Current statusJul 24, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 500
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 500
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2413.jpg

Downloads & links

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Map

FileDownload / File: emd_2413.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram asymmetric average of 206 selected virus particles attached to membrane.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.25 Å/pix.
x 128 pix.
= 800. Å		6.25 Å/pix.
x 128 pix.
= 800. Å		6.25 Å/pix.
x 128 pix.
= 800. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 500.0 / Movie #1: 500
Minimum - Maximum-0.08743927 - 949.828125
Average (Standard dev.)148.817459109999987 (±204.102935790000004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 800.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.256.256.25
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z800.000800.000800.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.087949.828148.817

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Supplemental data

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Sample components

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Entire : selected "best" average 135S poliovirus - membrane complex

EntireName: selected "best" average 135S poliovirus - membrane complex
Components
  • Sample: selected "best" average 135S poliovirus - membrane complex
  • Virus: Human poliovirus 1 Mahoney

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Supramolecule #1000: selected "best" average 135S poliovirus - membrane complex

SupramoleculeName: selected "best" average 135S poliovirus - membrane complex
type: sample / ID: 1000
Oligomeric state: one particle connects to one membrane at 2 sites
Number unique components: 1

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1
Details: The particle is in the expanded (135S) state, and connected to the membrane.
NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Sci species serotype: PV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 8.5 MDa / Theoretical: 8.5 MDa
Virus shellShell ID: 1 / Diameter: 330 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.3 / Details: 50mM Hepes, 50mM NaCl
GridDetails: 200 mesh copper Quantifoil grids (R2/2) with 3 nm carbon support on top.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: 2 second blot

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Electron beam tilt params: 0
DateOct 10, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 60 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45454 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 50000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsall particles close to a membrane were averaged
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Software - Name: IMOD, PEET, BSOFT, EMAN2, SPARX / Number subtomograms used: 206

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