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- PDB-3jbm: Electron cryo-microscopy of a virus-like particle of orange-spott... -

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Basic information

Entry
Database: PDB / ID: 3jbm
TitleElectron cryo-microscopy of a virus-like particle of orange-spotted grouper nervous necrosis virus
Componentsvirus-like particle of orange-spotted grouper nervous necrosis virus
KeywordsVIRUS / virus-like particle / orange-spotted grouper nervous necrosis virus / betanodavirus
Specimen sourceEpinephelus coioides (orange-spotted grouper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsXie, J. / Li, K. / Gao, Y. / Huang, R. / Lai, Y. / Shi, Y. / Yang, S. / Zhu, G. / Zhang, Q. / He, J.
CitationJournal: Vet. Res. / Year: 2016
Title: Structural analysis and insertion study reveal the ideal sites for surface displaying foreign peptides on a betanodavirus-like particle.
Authors: Junfeng Xie / Kunpeng Li / Yuanzhu Gao / Runqing Huang / Yuxiong Lai / Yan Shi / Shaowei Yang / Guohua Zhu / Qinfen Zhang / Jianguo He
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 6, 2015 / Release: Oct 19, 2016
RevisionDateData content typeGroupProviderType
1.0Oct 19, 2016Structure modelrepositoryInitial release
1.1Oct 26, 2016Structure modelOther
1.2Feb 22, 2017Structure modelDatabase references

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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
  • EMDB-6453
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus


Theoretical massNumber of molelcules
Total (without water)111,3083
Polyers111,3083
Non-polymers00
Water0
1
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 60


Theoretical massNumber of molelcules
Total (without water)6,678,489180
Polyers6,678,489180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 5


  • icosahedral pentamer
  • 557 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)556,54115
Polyers556,54115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 6


  • icosahedral 23 hexamer
  • 668 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)667,84918
Polyers667,84918
Non-polymers00
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
6
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 60


  • crystal asymmetric unit, crystal frame
  • 6.68 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)6,678,489180
Polyers6,678,489180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide virus-like particle of orange-spotted grouper nervous necrosis virus / Coordinate model: Cα atoms only


Mass: 37102.719 Da / Num. of mol.: 3
Source: (gene. exp.) Epinephelus coioides (orange-spotted grouper)
Production host: Escherichia coli (E. coli)
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: Orange-spotted grouper nervous necrosis virus / Type: VIRUS / Source: NATURAL
Molecular weightValue: 6.8 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Virus host category: VERTEBRATES / Virus isolate: SPECIES / Virus type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Epinephelus coioides
Buffer solutionName: PBS buffer / Details: PBS buffer / pH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh Quantifoil copper grid with thin carbon support, glow discharged in air atmosphere
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 % / Method: blot for 5 min before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Feb 26, 2011 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 / Nominal defocus max: 2910 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 200000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 kelvins / Temperature (max): 105 kelvins / Temperature (min): 95 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2JSPR3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I
3D reconstructionMethod: Cross-common lines / Resolution: 3.9 Å / Resolution method: FSC 0.143 / Number of particles: 32000 / Actual pixel size: 0.933
Details: (Single particle details: The particles were selected manually.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingMethod: Local refinement / Ref space: REAL
Atomic model buildingPDB-ID: 4NWW
Number of atoms included #LASTProtein: 526 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 526

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