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

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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 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Mar 25, 2008 / Release: Apr 29, 2008 / Last modification: Feb 24, 2009

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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-1508
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Assembly

Deposited unit
A: VP1
B: VP1
T: VP3


Theoretical massNumber of molelcules
Total (without water)416,8713
Polyers416,8713
Non-polymers00
Water0
#1
A: VP1
B: VP1
T: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)25,012,275180
Polyers25,012,275180
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)2,084,35615
Polyers2,084,35615
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)2,501,22818
Polyers2,501,22818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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: 148561.656 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: 119747.945 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: CYTOPLASMIC POLYHEDROSIS VIRUS / Aggregation state: PARTICLE
Details of the virusVirus host category: insect cells / Virus host species: Bombyx mori / Virus isolate: STRAIN / Virus type: virion
Buffer solutionName: 10MM PBS
Sample preparationpH: 7.4 / Sample conc.: 3 mg/ml
Specimen supportDetails: THE VIRIONS WERE EMBEDDED IN A THIN LAYER OF VITREOUS ICE SUSPENDED ACROSS THE HOLES OF HOLEY CARBON FILMS FOR CRYOEM IMAGING.
VitrificationDetails: PLUNGED INTO LIQUID ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA
Details: SAMPLES WERE MAINTAINED AT 100K IN THE ELECTRON MICROSCOPE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/A2 / Illumination mode: LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 154380 X / Calibrated magnification: 154380 X / Nominal defocus max: 13 nm / Nominal defocus min: 15 nm / Cs: 2 mm
Specimen holderTemperature: 1 K
CameraType: TVIPS CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionNumber of particles: 12814
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 A / Nominal pixel size: 0.972 A/pix / Actual pixel size: 0.972 A/pix / CTF correction method: CTF CORRECTION OF EACH PARTICLE
Details: PRIOR TO THE MERGING OF PARTICLES FOR 3D RECONSTRUCTION, THE FOURIER TRANSFORM VALUES OF INDIVIDUAL IMAGES WERE CORRECTED FOR THE CTF.
Least-squares processHighest resolution: 3.88 A
Refine hist #LASTHighest resolution: 3.88 A
Number of atoms included #LASTProtein: 2199 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2199

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