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- PDB-3izx: 3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus -

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Basic information

Entry
Database: PDB / ID: 3izx
Title3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus
Components
  • Capsid protein VP1
  • Structural protein VP3Structure
  • Viral structural protein 5
KeywordsVIRUS / cytoplasmic polyhedrosis virus / 3D reconstruction / cryoEM / full atom model
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid
Similarity search - Function
: / Viral structural protein 5 / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 ...: / Viral structural protein 5 / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / : / : / CPV Capsid shell protein VP1, small protrusion domain / Inner layer core protein VP1-like, C-terminal
Similarity search - Domain/homology
Viral structural protein 5 / Capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYu, X. / Ge, P. / Jiang, J. / Atanasov, I. / Zhou, Z.H.
CitationJournal: Structure / Year: 2011
Title: Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses.
Authors: Xuekui Yu / Peng Ge / Jiansen Jiang / Ivo Atanasov / Z Hong Zhou /
Abstract: Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we ...Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we report a 3.1 Å resolution cryo electron microscopy structure of CPV and derive its atomic model, consisting of 60 turret proteins (TPs), 120 each of capsid shell proteins (CSPs) and large protrusion proteins (LPPs). Two unique segments of CSP contribute to CPV's stability: an inserted protrusion domain interacting with neighboring proteins, and an N-anchor tying up CSPs together through strong interactions such as β sheet augmentation. Without the need to interact with outer shell proteins, LPP retains only the N-terminal two-third region containing a conserved helix-barrel core and interacts exclusively with CSP. TP is also simplified, containing only domains involved in RNA capping. Our results illustrate how CPV proteins have evolved in a coordinative manner to economically carry out their conserved functions.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Aug 22, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

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  • 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-5256
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5


Theoretical massNumber of molelcules
Total (without water)517,1265
Polymers517,1265
Non-polymers00
Water0
1
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
x 60


Theoretical massNumber of molelcules
Total (without water)31,027,556300
Polymers31,027,556300
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: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
x 5


  • icosahedral pentamer
  • 2.59 MDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)2,585,63025
Polymers2,585,63025
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
x 6


  • icosahedral 23 hexamer
  • 3.1 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)3,102,75630
Polymers3,102,75630
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Structural protein VP3 / Structure


Mass: 120145.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q914N6
#2: Protein Capsid protein VP1 /


Mass: 148560.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6TS43
#3: Protein Viral structural protein 5


Mass: 49929.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: C6K2M8

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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: cytoplasmic polyhedrosis virus (CPV) / Type: VIRUS
Details: Icosahedral particle. CPV particles were purified from polyhedra.
Details of virusEmpty: NO / Enveloped: NO / Host category: INVERTERBRATES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4 / Details: 10mM PBS
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mM PBS
VitrificationCryogen name: ETHANE / Temp: 90 K / Humidity: 40 % / Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 12, 2010 / Details: Low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.75 mm
Astigmatism: objective lens astigmatism was corrected a t 150,000 magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: Eucentric / Temperature: 90 K / Tilt angle max: -9999 ° / Tilt angle min: -9999 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: IMIRS / Category: 3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: common line / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28993
Details: ( Details about the particle: 645 micrographs that clearly showed signals beyond 6 angstrom in their spectra )
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms32209 0 0 0 32209

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