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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
DescriptorVP1, VP3
KeywordsVIRUS / cytoplasmic polyhedrosis virus / capsid protein / turret protein / polyhedrin-binding domain / guanylyltransferase domain / icosahedral virus
Specimen sourceBombyx mori cypovirus 1 / virus / image: Bombyx mori
MethodElectron microscopy (3.88 Å resolution / Particle / Single particle)
AuthorsYu, X. / Jin, L. / Zhou, Z.H.
CitationNature, 2008, 453, 415-419

Nature, 2008, 453, 415-419 StrPapers
3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy.
Xuekui Yu / Lei Jin / Z Hong Zhou

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 25, 2008 / Release: Apr 29, 2008
RevisionDateData content typeGroupProviderType
1.0Apr 29, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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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-1508
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Assembly

Deposited unit
A: VP1
B: VP1
T: VP3


Theoretical massNumber of molelcules
Total (without water)416,8693
Polyers416,8693
Non-polymers00
Water0
#1
A: VP1
B: VP1
T: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)25,012,130180
Polyers25,012,130180
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: VP1
B: VP1
T: VP3
x 5


  • icosahedral pentamer
  • 2.08 MDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)2,084,34415
Polyers2,084,34415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#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
Polyers2,501,21318
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

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Components

#1: Polypeptide(L)VP1


Mass: 148560.859 Da / Num. of mol.: 2
Source: (natural) Bombyx mori cypovirus 1 / virus / image: Bombyx mori
References: UniProt: Q6TS43

Cellular component

#2: Polypeptide(L)VP3


Mass: 119747.117 Da / Num. of mol.: 1
Source: (natural) Bombyx mori cypovirus 1 / virus / image: Bombyx mori
References: UniProt: Q9E957

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: CYTOPLASMIC POLYHEDROSIS VIRUS / Type: VIRUS
Details of the virusVirus host category: INSECT / Virus isolate: STRAIN / Virus type: VIRION
EM virus natural hostOrganism: Bombyx mori
Buffer solutionName: 10MM PBS / Details: 10MM PBS / pH: 7.4
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
MicroscopyMicroscope model: 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 FIELD / Nominal magnification: 154380 / Calibrated magnification: 154380 / Nominal defocus max: 13 nm / Nominal defocus min: 15 nm / Cs: 2 mm
Specimen holderTemperature: 1 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 Å / Number of particles: 12814 / Nominal pixel size: 0.972 / Actual pixel size: 0.972
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
Least-squares processHighest resolution: 3.88 Å
Refine hist #LASTHighest resolution: 3.88 Å
Number of atoms included #LASTProtein: 2199 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2199

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