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- EMDB-6639: Cryo-electron microscopy of a deletion mutant (d385-399) of Flock... -

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Basic information

Entry
Database: EMDB / ID: 6639
TitleCryo-electron microscopy of a deletion mutant (d385-399) of Flock House virus VLP
KeywordsFlock House virus / VLP / gamma
SampleVirus-like particle of deletion mutant (d385-399) of Flock House virus
SourceFlock house virus / virus
Map dataReconstruction of deletion mutant (d385-399) Flock House virus VLP
Methodsingle particle (icosahedral) reconstruction, at 14.5 Å resolution
AuthorsBajaj S / Dey D / Kumar M / Banerjee M
CitationJ. Mol. Biol., 2016, 428, 3540-3556

J. Mol. Biol., 2016, 428, 3540-3556 StrPapers
Non-Enveloped Virus Entry: Structural Determinants and Mechanism of Functioning of a Viral Lytic Peptide.
Saumya Bajaj / Debajit Dey / Rohan Bhukar / Mohit Kumar / Manidipa Banerjee

DateDeposition: Apr 29, 2016 / Header (metadata) release: Jun 15, 2016 / Map release: Dec 28, 2016 / Last update: Apr 29, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_6639.map.gz (map file in CCP4 format, 221185 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1 Å/pix.
= 384. Å
384 pix
1 Å/pix.
= 384. Å
384 pix
1 Å/pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1 Å
Density
Contour Level:0.6 (by author), 0.6 (movie #1):
Minimum - Maximum-0.78284472 - 1.65642786
Average (Standard dev.)0.07824882 (0.2857343)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin-192-192-192
Limit191191191
Spacing384384384
CellA=B=C: 384 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-0.7831.6560.078

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Supplemental data

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Sample components

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Entire Virus-like particle of deletion mutant (d385-399) of Flock House virus

EntireName: Virus-like particle of deletion mutant (d385-399) of Flock House virus
Number of components: 1
Oligomeric State: 180 molecules of capsid protein make up one particle
MassTheoretical: 9 MDa

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Component #1: virus, Flock house virus

VirusName: Flock house virus / Class: VIRUS-LIKE PARTICLE
Details: Residues 385-399 of the capsid protein have been deleted
Empty: No / Enveloped: No / Isolate: SPECIES
MassTheoretical: 9 MDa
SpeciesSpecies: Flock house virus / virus
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Vector: pBacPAK9 / Cell of expression system: Sf21
Source (natural)Host Species: Costelytra zealandica / Host category: INVERTEBRATES
Shell #1Name of element: Alpha / Diameter: 336 Å / T number(triangulation number): 3

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2.5 mg/ml / Buffer solution: 50 mM HEPES, 5mM CaCl2 / pH: 7.4
Support film300 mesh copper, Quantifoil R2/2 grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 %
Method: Blot for 3 seconds at a blot force of 0 before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jan 8, 2016
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 80,000x magnification
Cs: 1.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 94 K ( 77 - 97 K)
CameraDetector: FEI EAGLE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1199 / Bit depth: 2

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of class averages: 82 / Applied symmetry: I (icosahedral) / Number of projections: 20199
Details: Particles were boxed using the "Swarm mode" of e2boxer.py. Initial model generated by imposing icosahedral symmetry, and 3D refinement using e2refine_easy.py
3D reconstructionAlgorithm: Monte Carlo method (EMAN2) / Software: EMAN2 / CTF correction: Each particle / Resolution: 14.5 Å / Resolution method: FSC 0.143, gold-standard
FSC plot (resolution assessment)

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