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- EMDB-1939: Rabbit Hemorrhagic Disease Virus (RHDV)capsid calculated from mer... -

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Basic information

Database: EMDB / ID: 1939
TitleRabbit Hemorrhagic Disease Virus (RHDV)capsid calculated from merged wt, L17 and N42 data sets
Map dataRHDV Virus like particle capsid calculated from merged wt, L17 and L42 data sets
SampleRHDV Virus Like Particle capsid calculated from merged wt, L17 and L42 data sets:
Keywordscage design / molecular switch / protein engineering / structural polymorphism / virus assembly
SourceRabbit hemorrhagic disease virus (VP1)
Methodsingle particle reconstruction / cryo EM / negative staining / 8.9 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

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

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Fileemd_1939.map.gz (map file in CCP4 format, 328235 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
438 pix
1.4 Å/pix.
= 613.2 Å
438 pix
1.4 Å/pix.
= 613.2 Å
438 pix
1.4 Å/pix.
= 613.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Contour Level:0.55 (by author), 0.55 (movie #1):
Minimum - Maximum-1.12455976 - 2.40382743
Average (Standard dev.)0.00659150 (0.23046859)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 613.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z438438438
origin x/y/z0.0000.0000.000
length x/y/z613.200613.200613.200
start NX/NY/NZ-56-56-55
MAP C/R/S123
start NC/NR/NS-219-219-219
D min/max/mean-1.1252.4040.007

Supplemental data

Sample components

Entire RHDV Virus Like Particle capsid calculated from merged wt, L17 an...

EntireName: RHDV Virus Like Particle capsid calculated from merged wt, L17 and L42 data sets
Number of components: 1 / Oligomeric State: Icosahedral virus
MassTheoretical: 10.8 MDa

Component #1: virus, Rabbit hemorrhagic disease virus

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

Experimental details

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

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

Image acquisition

Image acquisitionNumber of digital images: 229 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 23606 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection Matching / Software: Xmipp / CTF correction: Phase flipping & amplitude decay / Resolution: 8.9 Å / Resolution method: FSC 0.5

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