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- EMDB-3599: Snake Adenovirus type 1 -

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Basic information

Entry
Database: EMDB / ID: 3599
TitleSnake Adenovirus type 1
Map dataSnake Adenovirus type 1
SampleSnake adenovirus 1:
virus
SourceSnake adenovirus 1
Methodsingle particle reconstruction / cryo EM / 10.9 Å resolution
AuthorsSan Martin C / Menendez-Conejero R
CitationJournal: Structure / Year: 2017
Title: Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.
Authors: Rosa Menéndez-Conejero / Thanh H Nguyen / Abhimanyu K Singh / Gabriela N Condezo / Rachel E Marschang / Mark J van Raaij / Carmen San Martín
Abstract: Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural ...Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors.
DateDeposition: Feb 23, 2017 / Header (metadata) release: Mar 15, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3599.map.gz (map file in CCP4 format, 271670 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
408 pix
2.75 Å/pix.
= 1122. Å
408 pix
2.75 Å/pix.
= 1122. Å
408 pix
2.75 Å/pix.
= 1122. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.75 Å
Density
Contour Level:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.021016927 - 0.08155101
Average (Standard dev.)0.0072269333 (0.017750613)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions408408408
Origin000
Limit407407407
Spacing408408408
CellA=B=C: 1122 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.752.752.75
M x/y/z408408408
origin x/y/z0.0000.0000.000
length x/y/z1122.0001122.0001122.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS408408408
D min/max/mean-0.0210.0820.007

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Supplemental data

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Sample components

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Entire Snake adenovirus 1

EntireName: Snake adenovirus 1 / Number of components: 1

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Component #1: virus, Snake adenovirus 1

VirusName: Snake adenovirus 1 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Snake adenovirus 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.8
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 12 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 300 - 3500 nm
Specimen HolderModel: OTHER
CameraDetector: KODAK SO-163 FILM

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2173
3D reconstructionResolution: 10.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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