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- PDB-6h2b: Structure of the Macrobrachium rosenbergii Nodavirus -

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Basic information

Entry
Database: PDB / ID: 6h2b
TitleStructure of the Macrobrachium rosenbergii Nodavirus
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Nodavirus / Capsid / Virion
Function / homologyViral coat protein subunit / Capsid protein
Function and homology information
Specimen sourceMacrobrachium rosenbergii nodavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.28 Å resolution
AuthorsHo, K.H. / Gabrielsen, M. / Beh, P.L. / Kueh, C.L. / Thong, Q.X. / Streetley, J. / Tan, W.S. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2018 / Release: Oct 31, 2018

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9319
Polyers124,6913
Non-polymers2406
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,495,875540
Polyers7,481,447180
Non-polymers14,428360
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 625 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)624,65645
Polyers623,45415
Non-polymers1,20230
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 750 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)749,58854
Polyers748,14518
Non-polymers1,44336
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide Capsid protein / Capsid


Mass: 41563.594 Da / Num. of mol.: 3 / Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Gene: CP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: X2FE19
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Macrobrachium rosenbergii nodavirus / Type: VIRUS / Details: Capsid protein was expressed in Sf9 cells / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Macrobrachium rosenbergii nodavirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Macrobrachium rosenbergii
Virus shellName: Capsid / Diameter: 400 nm / Triangulation number (T number): 3
Buffer solutionDetails: 20 mM HEPES, 100 mM NaCl pH 7.4 / pH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 47170 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2459
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 20 / Used frames/image: 2-20

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION2.1CTF correction
7Cootmodel fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELIONclassification
12RELION2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Automated particle picking in Relion 2.1 / Number of particles selected: 60939
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 40883 / Algorithm: BACK PROJECTION / Details: Standard Relion workflow for icosahedral particle. / Symmetry type: POINT
Atomic model buildingDetails: 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 b value: 140 / Ref protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00778004
ELECTRON MICROSCOPYf_angle_d0.843140750
ELECTRON MICROSCOPYf_dihedral_angle_d8.81631614
ELECTRON MICROSCOPYf_chiral_restr0.0596381
ELECTRON MICROSCOPYf_plane_restr0.00412283

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