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- EMDB-7941: Fako virus empty particles aligned to the best decoy map (asymmet... -

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Basic information

Entry
Database: EMDB / ID: 7941
TitleFako virus empty particles aligned to the best decoy map (asymmetric reconstruction) showing the locations of the polymerase complexes
Map dataAsymmetric reconstruction of Fako virus empty particles aligned to the best decoy map, showing the locations of the polymerase complexes
SampleFako virus:
virus / major capsid protein / RNA-dependent RNA polymerase / turret / clamp / accessory NTPase
SourceFako virus
Methodsingle particle reconstruction / cryo EM
AuthorsKaelber JT / Jiang W / Weaver SC / Auguste AJ / Chiu W
CitationJournal: To be Published
Title: The polymerase organization of Fako virus
Authors: Kaelber JT / Jiang W / Weaver SC / Auguste AJ / Chiu W
DateDeposition: May 26, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 30
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7941.map.gz (map file in CCP4 format, 265721 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
405 pix
2.14 Å/pix.
= 867.51 Å
405 pix
2.14 Å/pix.
= 867.51 Å
405 pix
2.14 Å/pix.
= 867.51 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.142 Å
Density
Contour Level:30.0 (by author), 30 (movie #1):
Minimum - Maximum-66.408910000000006 - 99.882959999999997
Average (Standard dev.)0.61569375 (7.19561)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions405405405
Origin-202.0-202.0-202.0
Limit202.0202.0202.0
Spacing405405405
CellA=B=C: 867.51 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1422.1422.142
M x/y/z405405405
origin x/y/z0.0000.0000.000
length x/y/z867.510867.510867.510
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-202-202-202
NC/NR/NS405405405
D min/max/mean-66.40999.8830.616

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Supplemental data

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Sample components

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Entire Fako virus

EntireName: Fako virus / Number of components: 6

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Component #1: virus, Fako virus

VirusName: Fako virus / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 43 MDa
SpeciesSpecies: Fako virus / Strain: CSW77
Source (natural)Host Species: Culicinae

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Component #2: protein, major capsid protein

ProteinName: major capsid protein / Recombinant expression: No
SourceSpecies: Fako virus / Strain: CSW77

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Component #3: protein, RNA-dependent RNA polymerase

ProteinName: RNA-dependent RNA polymerase / Recombinant expression: No
SourceSpecies: Fako virus / Strain: CSW77

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Component #4: protein, turret

ProteinName: turret / Recombinant expression: No
SourceSpecies: Fako virus / Strain: CSW77

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Component #5: protein, clamp

ProteinName: clamp / Recombinant expression: No
SourceSpecies: Fako virus / Strain: CSW77

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Component #6: protein, accessory NTPase

ProteinName: accessory NTPase / Recombinant expression: No
SourceSpecies: Fako virus / Strain: CSW77

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.8
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 4.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: JEOL 3200FSC CRYOHOLDER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 2400

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 4886
3D reconstructionAlgorithm: FOURIER SPACE / Software: jspr / Resolution method: OTHER
Details: The reconstruction method used does not preserve the independence of half-sets. As such, the Fourier shell correlation between half-sets is a biased measure and resolution is not calculated.

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