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- EMDB-1934: L17 Rabbit Hemorrhagic Disease Virus (RHDV)capsid -

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Basic information

Entry
Database: EMDB / ID: 1934
TitleL17 Rabbit Hemorrhagic Disease Virus (RHDV)capsid
Map dataRHDV L17 chimeric protein VP1 Virus Like Particle
SampleRHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RHDV with a 17 residues insertion in the P domain:
virus
Keywordscage design / molecular switch / protein engineering / structural polymorphism / virus assembly
SourceRabbit hemorrhagic disease virus (VP1-L17)
Methodsingle particle reconstruction / cryo EM / negative staining / 9.9 Å resolution
AuthorsLuque D / Gonzalez JM / Gomez-Blanco J / Marabini R / Chichon J / Mena I / Angulo I / Carrascosa JL / Verdaguer N / Trus BL / Barcena J / Caston JR
CitationJournal: J. Virol. / Year: 2012
Title: Epitope insertion at the N-terminal molecular switch of the rabbit hemorrhagic disease virus T = 3 capsid protein leads to larger T = 4 capsids.
Authors: Daniel Luque / José M González / Josué Gómez-Blanco / Roberto Marabini / Javier Chichón / Ignacio Mena / Iván Angulo / José L Carrascosa / Nuria Verdaguer / Benes L Trus / Juan Bárcena / José R Castón
DateDeposition: Jul 19, 2011 / Header (metadata) release: Jul 29, 2011 / Map release: May 17, 2012 / Last update: Oct 10, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

Fileemd_1934.map.gz (map file in CCP4 format, 41031 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
219 pix
2.8 Å/pix.
= 613.2 Å
219 pix
2.8 Å/pix.
= 613.2 Å
219 pix
2.8 Å/pix.
= 613.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:3.4 (by author), 3.4 (movie #1):
Minimum - Maximum-5.95444059 - 15.18414402
Average (Standard dev.)0.29703432 (1.56935835)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions219219219
Origin-109-109-109
Limit109109109
Spacing219219219
CellA=B=C: 613.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z219219219
origin x/y/z0.0000.0000.000
length x/y/z613.200613.200613.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-109-109-109
NC/NR/NS219219219
D min/max/mean-5.95415.1840.297

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Supplemental data

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Sample components

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Entire RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RH...

EntireName: RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RHDV with a 17 residues insertion in the P domain
Number of components: 1 / Oligomeric State: icosahedral
MassTheoretical: 10.8 MDa

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Component #1: virus, Rabbit hemorrhagic disease virus

VirusName: Rabbit hemorrhagic disease virus / a.k.a: VP1-L17 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 60 kDa
SpeciesSpecies: Rabbit hemorrhagic disease virus (VP1-L17)
Source (natural)Host Species: Oryctolagus cuniculus (rabbit) / Host category: VERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionBuffer solution: 200 mM Na2PO4, 100 mM NaCl / pH: 6
Support filmR 2/2 Quantifoil grids
StainingSamples were applied to grids, blotted and plunged into liquid ethane
VitrificationInstrument: NONE / 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: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 77 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7209 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay / Resolution: 9.9 Å / Resolution method: FSC 0.5

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