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

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Basic information

Database: EMDB / ID: 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
SourceMacrobrachium rosenbergii nodavirus
Methodsingle particle reconstruction / cryo EM / 3.28 Å resolution
AuthorsHo KH / Gabrielsen M / Beh PL / Kueh CL / Thong QX / Streetley J / Tan WS / Bhella D
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
Validation ReportPDB-ID: 6h2b

SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Oct 31, 2018 / Last update: Oct 31, 2018

Structure visualization

  • 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:
Supplemental images

Downloads & links


Fileemd_0129.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.06 Å/pix.
= 542.72 Å
512 pix
1.06 Å/pix.
= 542.72 Å
512 pix
1.06 Å/pix.
= 542.72 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.08820353 - 0.15871026
Average (Standard dev.)0.00086273794 (0.006595679)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 542.72 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
D min/max/mean-0.0880.1590.001

Supplemental data

Sample components

Entire Macrobrachium rosenbergii nodavirus

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

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
Shell #1Name of element: Capsid / Diameter: 400.0 Å / T number(triangulation number): 3

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)

Component #3: ligand, CALCIUM ION

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

Experimental details

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).

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
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2459
Raw dataEMPIAR-10203 (Title: Structure of the Macrobrachium rosenbergii Nodavirus: A new genus within the Nodaviridae?
Data size: 130.4
Data #1: Motion corrected micrographs of Macrobrachium rosenbergii nodavirus virus-like particles [micrographs - single frame])

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)

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: 14
Output model

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