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- EMDB-8983: Asymmetric cryo-EM structure of immature Kunjin virus -

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Basic information

Entry
Database: EMDB / ID: EMD-8983
TitleAsymmetric cryo-EM structure of immature Kunjin virus
Map dataAsymmetric reconstruction of immature Kunjin virus.
Sample
  • Virus: Kunjin virus (STRAIN MRM61C)
    • Organelle or cellular component: Glycoprotein shell
    • Organelle or cellular component: Nucleocapsid core
Biological speciesKunjin virus (STRAIN MRM61C)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsTherkelsen MD / Klose T / Vago F / Jiang W / Rossmann MG / Kuhn RJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Flaviviruses have imperfect icosahedral symmetry.
Authors: Matthew D Therkelsen / Thomas Klose / Frank Vago / Wen Jiang / Michael G Rossmann / Richard J Kuhn /
Abstract: Flaviviruses assemble initially in an immature, noninfectious state and undergo extensive conformational rearrangements to generate mature virus. Previous cryo-electron microscopy (cryo-EM) ...Flaviviruses assemble initially in an immature, noninfectious state and undergo extensive conformational rearrangements to generate mature virus. Previous cryo-electron microscopy (cryo-EM) structural studies of flaviviruses assumed icosahedral symmetry and showed the concentric organization of the external glycoprotein shell, the lipid membrane, and the internal nucleocapsid core. We show here that when icosahedral symmetry constraints were excluded in calculating the cryo-EM reconstruction of an immature flavivirus, the nucleocapsid core was positioned asymmetrically with respect to the glycoprotein shell. The core was positioned closer to the lipid membrane at the proximal pole, and at the distal pole, the outer glycoprotein spikes and inner membrane leaflet were either perturbed or missing. In contrast, in the asymmetric reconstruction of a mature flavivirus, the core was positioned concentric with the glycoprotein shell. The deviations from icosahedral symmetry demonstrated that the core and glycoproteins have varied interactions, which likely promotes viral assembly and budding.
History
DepositionJul 21, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseNov 21, 2018-
UpdateNov 21, 2018-
Current statusNov 21, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8983.png

Downloads & links

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Map

FileDownload / File: emd_8983.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of immature Kunjin virus.
Voxel sizeX=Y=Z: 3.24 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0339802 - 0.07238753
Average (Standard dev.)0.000027152577 (±0.0053210477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 1036.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.243.243.24
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1036.8001036.8001036.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0340.0720.000

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Supplemental data

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Sample components

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Entire : Kunjin virus (STRAIN MRM61C)

EntireName: Kunjin virus (STRAIN MRM61C)
Components
  • Virus: Kunjin virus (STRAIN MRM61C)
    • Organelle or cellular component: Glycoprotein shell
    • Organelle or cellular component: Nucleocapsid core

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Supramolecule #1: Kunjin virus (STRAIN MRM61C)

SupramoleculeName: Kunjin virus (STRAIN MRM61C) / type: virus / ID: 1 / Parent: 0
Details: Immature Kunjin virus purified from ammonium chloride-treated C6/36 cells.
NCBI-ID: 11078 / Sci species name: Kunjin virus (STRAIN MRM61C) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: capsid shell / Diameter: 560.0 Å / T number (triangulation number): 3

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Supramolecule #2: Glycoprotein shell

SupramoleculeName: Glycoprotein shell / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Kunjin virus (STRAIN MRM61C)

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Supramolecule #3: Nucleocapsid core

SupramoleculeName: Nucleocapsid core / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Source (natural)Organism: Kunjin virus (STRAIN MRM61C)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridMaterial: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3 / Details: Blot for 6 seconds before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 387 / Average electron dose: 24.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1) / Number images used: 7396
FSC plot (resolution estimation)

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