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

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Basic information

Entry
Database: EMDB / ID: EMD-1934
TitleL17 Rabbit Hemorrhagic Disease Virus (RHDV)capsid
Map dataRHDV L17 chimeric protein VP1 Virus Like Particle
Sample
  • Sample: RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RHDV with a 17 residues insertion in the P domain
  • Virus: Rabbit hemorrhagic disease virus
Keywordscage design / molecular switch / protein engineering / structural polymorphism / virus assembly
Biological speciesRabbit hemorrhagic disease virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.9 Å
AuthorsLuque D / Gonzalez JM / Gomez-Blanco J / Marabini R / Chichon J / Mena I / Angulo I / Carrascosa JL / Verdaguer N / Trus BL ...Luque 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 ...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 /
Abstract: Viruses need only one or a few structural capsid proteins to build an infectious particle. This is possible through the extensive use of symmetry and the conformational polymorphism of the structural ...Viruses need only one or a few structural capsid proteins to build an infectious particle. This is possible through the extensive use of symmetry and the conformational polymorphism of the structural proteins. Using virus-like particles (VLP) from rabbit hemorrhagic disease virus (RHDV) as a model, we addressed the basis of calicivirus capsid assembly and their application in vaccine design. The RHDV capsid is based on a T=3 lattice containing 180 identical subunits (VP1). We determined the structure of RHDV VLP to 8.0-Å resolution by three-dimensional cryoelectron microscopy; in addition, we used San Miguel sea lion virus (SMSV) and feline calicivirus (FCV) capsid subunit structures to establish the backbone structure of VP1 by homology modeling and flexible docking analysis. Based on the three-domain VP1 model, several insertion mutants were designed to validate the VP1 pseudoatomic model, and foreign epitopes were placed at the N- or C-terminal end, as well as in an exposed loop on the capsid surface. We selected a set of T and B cell epitopes of various lengths derived from viral and eukaryotic origins. Structural analysis of these chimeric capsids further validates the VP1 model to design new chimeras. Whereas most insertions are well tolerated, VP1 with an FCV capsid protein-neutralizing epitope at the N terminus assembled into mixtures of T=3 and larger T=4 capsids. The calicivirus capsid protein, and perhaps that of many other viruses, thus can encode polymorphism modulators that are not anticipated from the plane sequence, with important implications for understanding virus assembly and evolution.
History
DepositionJul 19, 2011-
Header (metadata) releaseJul 29, 2011-
Map releaseMay 17, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

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

emd_1934.png

Downloads & links

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Map

FileDownload / File: emd_1934.map.gz / Format: CCP4 / Size: 39.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRHDV L17 chimeric protein VP1 Virus Like Particle
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-5.95444059 - 15.18414402
Average (Standard dev.)0.29703432 (±1.56935835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-109-109-109
Dimensions219219219
Spacing219219219
CellA=B=C: 613.2 Å
α=β=γ: 90.0 °

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
Components
  • Sample: RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RHDV with a 17 residues insertion in the P domain
  • Virus: Rabbit hemorrhagic disease virus

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Supramolecule #1000: RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RH...

SupramoleculeName: RHDV L17 VP1 Virus Like Particle. Chimeric protein of VP1 from RHDV with a 17 residues insertion in the P domain
type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 10.8 MDa

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Supramolecule #1: Rabbit hemorrhagic disease virus

SupramoleculeName: Rabbit hemorrhagic disease virus / type: virus / ID: 1 / Name.synonym: VP1-L17 / NCBI-ID: 11976 / Sci species name: Rabbit hemorrhagic disease virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: VP1-L17
Host (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: VERTEBRATES
Molecular weightTheoretical: 60 KDa
Virus shellShell ID: 1 / Diameter: 400 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6 / Details: 200 mM Na2PO4, 100 mM NaCl
StainingType: NEGATIVE
Details: Samples were applied to grids, blotted and plunged into liquid ethane
GridDetails: R 2/2 Quantifoil grids
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 77 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping & amplitude decay
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp / Number images used: 7209

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