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

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Basic information

Entry
Database: EMDB / ID: EMD-0129
TitleStructure of the Macrobrachium rosenbergii Nodavirus
Map dataNone
Sample
  • Virus: Macrobrachium rosenbergii nodavirus
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: CALCIUM IONCalcium
Function / homologyViral coat protein subunit / Capsid protein alpha
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.
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
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  • Surface view colored by radius
  • Surface level: 0.02
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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 modelsPDB-6h2b
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0129.png

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)
AnnotationNone
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
Components
  • Virus: Macrobrachium rosenbergii nodavirus
    • Protein or peptide: Capsid proteinCapsid
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Macrobrachium rosenbergii nodavirus

SupramoleculeName: Macrobrachium rosenbergii nodavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Capsid protein was expressed in Sf9 cells / NCBI-ID: 222557 / Sci species name: Macrobrachium rosenbergii nodavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macrobrachium rosenbergii (giant freshwater prawn)
Host systemOrganism: Spodoptera frugiperda (fall armyworm)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macrobrachium rosenbergii nodavirus
Molecular weightTheoretical: 41.563594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MARGKQNSNQ AQNNSNANGK RRKRSRRNRN PQTIPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLTDSKSR ILVKQPISAS SFLGTRISGL SQFWERYRWH KAAVRYVPAV PNTLACQLIG YIDTDPLDDP NVILDVDQLL R QATSQVGA ...String:
MARGKQNSNQ AQNNSNANGK RRKRSRRNRN PQTIPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLTDSKSR ILVKQPISAS SFLGTRISGL SQFWERYRWH KAAVRYVPAV PNTLACQLIG YIDTDPLDDP NVILDVDQLL R QATSQVGA RQWNFSDTTT IPLIVRRDDQ LYYTGQDKEN VRFSQQGVFY LLQVTTLLNI SGEAITNDLI SGSLYLDWVC GF SMPQINP TPVEISQLTY NADTIGNWVP PTELNQTYTQ DITGLKPNSK FIIVPYMDRT SSEVLQKCTI TCNEVNAVGS ISY FDTNDI KCNGYITFQA NNIGEATFTL VTDYKGVTDA KPYQYRIIRA IVGNN

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES, 100 mM NaCl pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K
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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 2459 / Average exposure time: 5.0 sec. / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 60939 / Details: Automated particle picking in Relion 2.1
CTF correctionSoftware - Name: RELION (ver. 2.1)
Startup modelType of model: EMDB MAP
EMDB ID:

3655


Details: our previously calculated intermediate resolution structure of the same VLP was used to start data processing.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Details: Standard Relion workflow for icosahedral particle. / Number images used: 40883
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModel 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.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 140
Output model

PDB-6h2b:
Structure of the Macrobrachium rosenbergii Nodavirus

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