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- PDB-6jjc: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -

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Entry
Database: PDB / ID: 6jjc
TitleCryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Giant freshwater prawn Macrobrachium rosenbergii / T=3 icosahedral particle / Double-stranded RNA virus / Canonical jelly-roll beta-barrel fold
Function / homologyViral coat protein subunit / Capsid protein
Function and homology information
Specimen sourceMacrobrachium rosenbergii nodavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsChang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y.
Funding supportTaiwan , 7件
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)MOST 103-2321-B-001-048Taiwan
Ministry of Science and Technology (Taiwan)MOST 104-2321-B-001-019Taiwan
Ministry of Science and Technology (Taiwan)MOST 105-2321-B-001-009Taiwan
Ministry of Science and Technology (Taiwan)MOST 106-0210-01-15-02Taiwan
Ministry of Science and Technology (Taiwan)MOST 106-0210-01-15-04Taiwan
Ministry of Science and Technology (Taiwan)MOST 107-0210-01-19-01Taiwan
Ministry of Science and Technology (Taiwan)MOST 107-0210-01-19-02Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP
Authors: Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 25, 2019 / Release: May 1, 2019Array

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9706
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-9706
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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)124,72210
Polymers124,4423
Non-polymers2817
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,483,348600
Polymers7,466,515180
Non-polymers16,833420
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
  • 624 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)623,61250
Polymers622,21015
Non-polymers1,40335
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 748 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)748,33560
Polymers746,65218
Non-polymers1,68342
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein/peptide Capsid protein / Capsid


Mass: 41480.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15BP6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca / Calcium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: VirusesVirus / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 7.452 MDa / Experimental value: NO
Source (natural)Organism: Viruses / Strain: Macrobrachium rosenbergii nodavirus (Taiwan strain)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pETDuet-1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Macrobrachium rosenbergii / Strain: Taiwan strain
Virus shellName: capsid proteinCapsid / Diameter: 400 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component

Buffer-ID: 1

IDConc.NameFormula
150 mMSodium chlorideNaCl
250 mMTrisTris
31 mMCalcium chlorideCaCl2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 274 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Calibrated defocus min: 450 nm / Calibrated defocus max: 3370 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 37 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1353
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
2EPU1.11.1.50RELimage acquisition
4RELION2CTF correction
7UCSF Chimera1.11.2model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX3374model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 19049
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19049 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

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