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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: EMD-7941
TitleFako virus empty particles aligned to the best decoy map (asymmetric reconstruction) showing the locations of the polymerase complexes
Map data
SampleFako virus:
virus / major capsid protein / RNA-dependent RNA polymerase / turret / clamp / accessory NTPase
Biological speciesFako virus
Methodsingle particle reconstruction / cryo EM
AuthorsKaelber JT / Jiang W / Weaver SC / Auguste AJ / Chiu W
CitationJournal: Structure / Year: 2020
Title: Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus.
Authors: Jason T Kaelber / Wen Jiang / Scott C Weaver / Albert J Auguste / Wah Chiu /
Abstract: Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle ...Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle reconstruction encounters difficulties resolving structures such as the intraparticle polymerase complex because refinement can converge to an incorrect map and because the map could depict a nonrepresentative subset of particles or an average of heterogeneous particles. Using the nine-segmented Fako virus, we tested hypotheses for the arrangement and number of polymerase complexes within the virion by measuring how well each hypothesis describes the set of cryoelectron microscopy images of individual viral particles. We find that the polymerase complex in Fako virus binds at ten possible sites despite having only nine genome segments. A single asymmetric configuration describes the arrangement of these complexes in both virions and genome-free capsids. Similarities between the arrangements of Reoviridae with 9, 10, and 11 segments indicate the generalizability of this architecture.
History
DepositionMay 26, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJan 16, 2019-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7941.map.gz / Format: CCP4 / Size: 253.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.14 Å/pix.
x 405 pix.
= 867.51 Å
2.14 Å/pix.
x 405 pix.
= 867.51 Å
2.14 Å/pix.
x 405 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 LevelBy AUTHOR: 30.0 / Movie #1: 30
Minimum - Maximum-66.408910000000006 - 99.882959999999997
Average (Standard dev.)0.61569375 (±7.19561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-202-202-202
Dimensions405405405
Spacing405405405
CellA=B=C: 867.51 Å
α=β=γ: 90.0 °

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
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 (mosquito)

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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: 30 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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