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- EMDB-0129: Structure of the Macrobrachium rosenbergii Nodavirus -

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Entry
Database: EMDB / ID: EMD-0129
TitleStructure of the Macrobrachium rosenbergii Nodavirus
Map data
SampleMacrobrachium rosenbergii nodavirus:
virus / Capsid proteinCapsid / ligand
Function / homologyViral coat protein subunit / Capsid protein
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsHo KH / Gabrielsen M / Beh PL / Kueh CL / Thong QX / Streetley J / Tan WS / Bhella D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_12014/7 United Kingdom
CitationJournal: PLoS Biol. / Year: 2018
Title: Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?
Authors: Kok Lian Ho / Mads Gabrielsen / Poay Ling Beh / Chare Li Kueh / Qiu Xian Thong / James Streetley / Wen Siang Tan / David Bhella /
Abstract: Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many ...Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.
Validation ReportPDB-ID: 6h2b

SummaryFull reportAbout validation report
History
DepositionJul 13, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseOct 31, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6h2b
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6h2b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0129.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å
1.06 Å/pix.
x 512 pix.
= 542.72 Å
1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08820353 - 0.15871026
Average (Standard dev.)0.00086273794 (±0.006595679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z542.720542.720542.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.0880.1590.001

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Supplemental data

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Sample components

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Entire Macrobrachium rosenbergii nodavirus

EntireName: Macrobrachium rosenbergii nodavirus / Details: Capsid protein was expressed in Sf9 cells / Number of components: 3

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Component #1: virus, Macrobrachium rosenbergii nodavirus

VirusName: Macrobrachium rosenbergii nodavirus / Class: VIRUS-LIKE PARTICLE / Details: Capsid protein was expressed in Sf9 cells / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Macrobrachium rosenbergii nodavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)
Source (natural)Host Species: Macrobrachium rosenbergii (giant freshwater prawn)
Shell #1Name of element: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3

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Component #2: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 41.563594 kDa
SourceSpecies: Macrobrachium rosenbergii nodavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: ligand, CALCIUM ION

LigandName: CALCIUM IONCalcium / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / Buffer solution: 20 mM HEPES, 100 mM NaCl pH 7.4 / pH: 7.4
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47170.0 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2459

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 40883
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Standard Relion workflow for icosahedral particle.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Model built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-135 and 232-243. This served as the starting point for manual model building. The model was then subjected to real space refinement using Phenix.
Overall bvalue: 140
Output model

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