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- EMDB-2025: CryoEM 3D reconstruction of full Triatoma Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-2025
TitleCryoEM 3D reconstruction of full Triatoma Virus
Map dataFull TrV particle 3D reconstruction
Sample
  • Sample: Full Triatoma Virus
  • Virus: Triatoma virus
KeywordsTriatoma virus / Dicistrovirus / 3D reconstruction
Biological speciesTriatoma virus
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 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 20, 2012-
Map releaseJan 23, 2013-
UpdateOct 8, 2014-
Current statusOct 8, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 37
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 37
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2025.png

Downloads & links

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Map

FileDownload / File: emd_2025.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull TrV particle 3D reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.75 Å/pix.
x 255 pix.
= 446.25 Å		1.75 Å/pix.
x 255 pix.
= 446.25 Å		1.75 Å/pix.
x 255 pix.
= 446.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 37.0 / Movie #1: 37
Minimum - Maximum-122.0 - 212.0
Average (Standard dev.)5.68131351 (±30.804971689999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions255255255
Spacing255255255
CellA=B=C: 446.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.751.751.75
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z446.250446.250446.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS255255255
D min/max/mean-122.000212.0005.681

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Supplemental data

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Sample components

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Entire : Full Triatoma Virus

EntireName: Full Triatoma Virus
Components
  • Sample: Full Triatoma Virus
  • Virus: Triatoma virus

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Supramolecule #1000: Full Triatoma Virus

SupramoleculeName: Full Triatoma Virus / 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 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: TrV
Host (natural)Organism: Triatoma infestans (insect) / 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

MicroscopeJEOL 2010F
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 25
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2 / Number images used: 1716

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