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- EMDB-5374: Structural basis for broad detection of genogroup II noroviruses ... -

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Entry
Database: EMDB / ID: EMD-5374
TitleStructural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle
Map dataSurface rendering of GII.10 norovirus VLP
Sample
  • Sample: GII.10 norovirus VLP
  • Virus: Norovirus genogroup GII.10
Keywordsnorovirus
Biological speciesNorovirus genogroup GII.10
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsHansman GS / Taylor DW / McLellan JS / Smith TJ / Georgiev I / Tame JRH / Park SY / Yamazaki M / Gondaira F / Miki M ...Hansman GS / Taylor DW / McLellan JS / Smith TJ / Georgiev I / Tame JRH / Park SY / Yamazaki M / Gondaira F / Miki M / Katayama K / Murata K / Kwong PD
CitationJournal: J Virol / Year: 2012
Title: Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle.
Authors: Grant S Hansman / David W Taylor / Jason S McLellan / Thomas J Smith / Ivelin Georgiev / Jeremy R H Tame / Sam-Yong Park / Makoto Yamazaki / Fumio Gondaira / Motohiro Miki / Kazuhiko ...Authors: Grant S Hansman / David W Taylor / Jason S McLellan / Thomas J Smith / Ivelin Georgiev / Jeremy R H Tame / Sam-Yong Park / Makoto Yamazaki / Fumio Gondaira / Motohiro Miki / Kazuhiko Katayama / Kazuyoshi Murata / Peter D Kwong /
Abstract: Human noroviruses are genetically and antigenically highly divergent. Monoclonal antibodies raised in mice against one kind of norovirus virus-like particle (VLP), however, were found to have broad ...Human noroviruses are genetically and antigenically highly divergent. Monoclonal antibodies raised in mice against one kind of norovirus virus-like particle (VLP), however, were found to have broad recognition. In this study, we present the crystal structure of the antigen-binding fragment (Fab) for one of these broadly reactive monoclonal antibodies, 5B18, in complex with the capsid-protruding domain from a genogroup II genotype 10 (GII.10) norovirus at 3.3-Å resolution and, also, the cryo-electron microscopy structure of the GII.10 VLP at ∼10-Å resolution. The GII.10 VLP structure was more similar in overall architecture to the GV.1 murine norovirus virion than to the prototype GI.1 human norovirus VLP, with the GII.10 protruding domain raised ∼15 Å off the shell domain and rotated ∼40° relative to the GI.1 protruding domain. In the crystal structure, the 5B18 Fab bound to a highly conserved region of the protruding domain. Based on the VLP structure, this region is involved in interactions with other regions of the capsid and is buried in the virus particle. Despite the occluded nature of the recognized epitope in the VLP structure, enzyme-linked immunosorbent assay (ELISA) binding suggested that the 5B18 antibody was able to capture intact VLPs. Together, the results provide evidence that the norovirus particle is capable of extreme conformational flexibility, which may allow for antibody recognition of conserved surfaces that would otherwise be buried on intact particles.
History
DepositionDec 20, 2011-
Header (metadata) releaseJan 9, 2012-
Map releaseJan 30, 2012-
UpdateFeb 8, 2012-
Current statusFeb 8, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.87
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.87
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5374.png

Downloads & links

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Map

FileDownload / File: emd_5374.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendering of GII.10 norovirus VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 250 pix.
= 600. Å		2.4 Å/pix.
x 250 pix.
= 600. Å		2.4 Å/pix.
x 250 pix.
= 600. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.87 / Movie #1: 2.87
Minimum - Maximum-6.03285646 - 14.81038094
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-125-125-125
Dimensions250250250
Spacing250250250
CellA=B=C: 600.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z600.000600.000600.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-6.03314.810-0.000

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Supplemental data

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Sample components

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Entire : GII.10 norovirus VLP

EntireName: GII.10 norovirus VLP
Components
  • Sample: GII.10 norovirus VLP
  • Virus: Norovirus genogroup GII.10

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Supramolecule #1000: GII.10 norovirus VLP

SupramoleculeName: GII.10 norovirus VLP / type: sample / ID: 1000 / Oligomeric state: icosahedral (T3) / Number unique components: 1
Molecular weightExperimental: 10 MDa / Theoretical: 10 MDa

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Supramolecule #1: Norovirus genogroup GII.10

SupramoleculeName: Norovirus genogroup GII.10 / type: virus / ID: 1 / Name.synonym: GII.10 Vietnam 026 VLP / NCBI-ID: 747305 / Sci species name: Norovirus genogroup GII.10 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: GII.10 Vietnam 026 VLP
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 10 MDa / Theoretical: 10 MDa
Virus shellShell ID: 1 / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.3 / Details: PBS
GridDetails: Quantifoil R1.2/1.3 Mo 200 mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: Vitrification instrument: FEI Vitrobot Mark IV. Quantifoil Mo 200 mesh holey carbon grid with a thin layer of carbon over the holes
Method: automatic blotting for 8 seconds

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Electron microscopy

MicroscopeJEOL 2200FS
DateJul 22, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected semi-automatically using the swarm program in EMAN2.
CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 8000

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