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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: 5380
TitleCryo-EM 3D reconstruction of empty Triatoma Virus (corresponding to a suspension of full TrV heated)
Map data3D reconstruction of empty TrV
SampleEmpty TrV particles:
virus
KeywordsTriatoma virus / Dicistrovirus / cryo-electron microscopy / 3D reconstruction / RNA delivery
SourceTriatoma virus (TrV)
Methodsingle particle reconstruction / cryo EM / 22 Å resolution
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
DateDeposition: Jan 6, 2012 / Header (metadata) release: Jan 13, 2012 / Map release: Feb 13, 2013 / Last update: Aug 14, 2013

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5380.map.gz (map file in CCP4 format, 64772 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
255 pix
1.77 Å/pix.
= 451.35 Å
255 pix
1.77 Å/pix.
= 451.35 Å
255 pix
1.77 Å/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
Contour Level:0.001 (by author), 0.001 (movie #1):
Minimum - Maximum-0.00255000 - 0.00416000
Average (Standard dev.)0.00003111 (0.00061384)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions255255255
Origin-127-107-127
Limit127147127
Spacing255255255
CellA=B=C: 451.35 Å
α=β=γ: 90.0 deg.

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 / Number of components: 1

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Component #1: virus, Triatoma virus

VirusName: Triatoma virus / a.k.a: TrV / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Triatoma virus (TrV)
Source (natural)Host category: INVERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: NMT (10 mM NaCl, 1 mM MgCl2, 50 mM Tris-HCl)
pH: 7.4
Support film400 mesh quantifoil grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: Vitrobot FEI

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200T
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: OTHER
LensMagnification: 38000 X (nominal), 39500 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4000 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 7 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 573 / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: EM3DR2 / Resolution: 22 Å / Resolution method: FSC 0.5

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