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- EMDB-5380: Cryo-EM 3D reconstruction of empty Triatoma Virus (corresponding ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5380
TitleCryo-EM 3D reconstruction of empty Triatoma Virus (corresponding to a suspension of full TrV heated)
Map data3D reconstruction of empty TrV
Sample
  • Sample: Empty TrV particles
  • Virus: Triatoma virus
KeywordsTriatoma virus / Dicistrovirus / cryo-electron microscopy / 3D reconstruction / RNA delivery
Biological speciesTriatoma virus
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsNeumann E / Agirre J / Goret G / Legoff M / Marti GA / Navaza J / Guerin DMA
CitationJournal: J Gen Virol / Year: 2013
Title: Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly.
Authors: J Agirre / G Goret / M LeGoff / R Sánchez-Eugenia / G A Marti / J Navaza / D M A Guérin / E Neumann /
Abstract: Triatoma virus (TrV) is a member of the insect virus family Dicistroviridae and consists of a small, non-enveloped capsid that encloses its positive-sense ssRNA genome. Using cryo-transmission ...Triatoma virus (TrV) is a member of the insect virus family Dicistroviridae and consists of a small, non-enveloped capsid that encloses its positive-sense ssRNA genome. Using cryo-transmission electron microscopy and three-dimensional reconstruction techniques combined with fitting of the available crystallographic models, this study analysed the capsids corresponding to mature and several RNA-empty TrV particles. After genome release, the resulting reconstruction of the empty capsids displayed no prominent conformational changes with respect to the full virion capsid. The results showed that RNA delivery led to empty capsids with an apparent overall intact protein shell and suggested that, in a subsequent step, empty capsids disassemble into small symmetrical particles. Contrary to what is observed upon genome release in mammalian picornaviruses, the empty TrV capsid maintained a protein shell thickness and size identical to that in full virions.
History
DepositionJan 6, 2012-
Header (metadata) releaseJan 13, 2012-
Map releaseFeb 13, 2013-
UpdateAug 14, 2013-
Current statusAug 14, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.001
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.001
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5380_1.tif

Downloads & links

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Map

FileDownload / File: emd_5380.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of empty TrV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 255 pix.
= 451.35 Å		1.77 Å/pix.
x 255 pix.
= 451.35 Å		1.77 Å/pix.
x 255 pix.
= 451.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001 / Movie #1: 0.001
Minimum - Maximum-0.00255 - 0.00416
Average (Standard dev.)0.00003111 (±0.00061384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-107-127
Dimensions255255255
Spacing255255255
CellA=B=C: 451.35 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z451.350451.350451.350
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-107-127-127
NC/NR/NS255255255
D min/max/mean-0.0030.0040.000

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Supplemental data

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Sample components

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Entire : Empty TrV particles

EntireName: Empty TrV particles
Components
  • Sample: Empty TrV particles
  • Virus: Triatoma virus

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Supramolecule #1000: Empty TrV particles

SupramoleculeName: Empty TrV particles / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Triatoma virus

SupramoleculeName: Triatoma virus / type: virus / ID: 1 / Name.synonym: TrV / NCBI-ID: 103442 / Sci species name: Triatoma virus / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes / Syn species name: TrV
Host (natural)synonym: INVERTEBRATES
Virus shellShell ID: 1 / T number (triangulation number): 1

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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: NMT (10 mM NaCl, 1 mM MgCl2, 50 mM Tris-HCl)
GridDetails: 400 mesh quantifoil grid
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot FEI

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 15
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 39500 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2 / Number images used: 573

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