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- PDB-3cnf: 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo... -

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Basic information

Entry
Database: PDB / ID: 3cnf
Title3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy
Components
  • VP1
  • VP3
KeywordsVIRUS / cytoplasmic polyhedrosis virus / capsid protein / turret protein / polyhedrin-binding domain / guanylyltransferase domain / icosahedral virus
Function / homology: / : / CPV Capsid shell protein VP1, small protrusion domain / Inner layer core protein VP1-like, C-terminal / T=2 icosahedral viral capsid / viral inner capsid / Capsid protein VP1 / VP3
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsYu, X. / Jin, L. / Zhou, Z.H.
CitationJournal: Nature / Year: 2008
Title: 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
Authors: Xuekui Yu / Lei Jin / Z Hong Zhou /
Abstract: Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell ...Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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-1508
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP1
T: VP3


Theoretical massNumber of molelcules
Total (without water)416,8693
Polymers416,8693
Non-polymers00
Water0
1
A: VP1
B: VP1
T: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)25,012,130180
Polymers25,012,130180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP1
T: VP3
x 5


  • icosahedral pentamer
  • 2.08 MDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)2,084,34415
Polymers2,084,34415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP1
T: VP3
x 6


  • icosahedral 23 hexamer
  • 2.5 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)2,501,21318
Polymers2,501,21318
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 VP1 / Coordinate model: Cα atoms only


Mass: 148560.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6TS43
#2: Protein VP3 / Coordinate model: Cα atoms only


Mass: 119747.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The cytoplasmic polyhedrosis virus was isolated and purified from infected Bombyx mori larvae.
Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q9E957

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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 VIRUSCypovirus / Type: VIRUS
Details of virusHost category: INSECT / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Bombyx mori
Buffer solutionName: 10MM PBS / pH: 7.4 / Details: 10MM PBS
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: THE VIRIONS WERE EMBEDDED IN A THIN LAYER OF VITREOUS ICE SUSPENDED ACROSS THE HOLES OF HOLEY CARBON FILMS FOR CRYOEM IMAGING.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Details: SAMPLES WERE MAINTAINED AT 100K IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 154380 X / Calibrated magnification: 154380 X / Nominal defocus max: 1300 nm / Nominal defocus min: 150 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

CTF correctionDetails: CTF CORRECTION OF EACH PARTICLE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 Å / Num. of particles: 12814 / Nominal pixel size: 0.972 Å / Actual pixel size: 0.972 Å
Details: PRIOR TO THE MERGING OF PARTICLES FOR 3D RECONSTRUCTION, THE FOURIER TRANSFORM VALUES OF INDIVIDUAL IMAGES WERE CORRECTED FOR THE CTF.
Symmetry type: POINT
RefinementHighest resolution: 3.88 Å
Refinement stepCycle: LAST / Highest resolution: 3.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 0 2199

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