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- EMDB-27559: Cryo-EM map of Chikungunya virus strain s27 -

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Basic information

Entry
Database: EMDB / ID: EMD-27559
TitleCryo-EM map of Chikungunya virus strain s27
Map dataChikungunya virus strain S27
Sample
  • Virus: Chikungunya virus strain S27-African prototype
Biological speciesChikungunya virus strain S27-African prototype
Methodsingle particle reconstruction / cryo EM / Resolution: 6.75 Å
AuthorsMangala Prasad V / Lee KK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM099989 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: Nat Commun / Year: 2022
Title: Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery.
Authors: Vidya Mangala Prasad / Jelle S Blijleven / Jolanda M Smit / Kelly K Lee /
Abstract: Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though ...Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.
History
DepositionJul 11, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateAug 31, 2022-
Current statusAug 31, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27559.png

Downloads & links

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Map

FileDownload / File: emd_27559.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya virus strain S27
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 400 pix.
= 1080. Å		2.7 Å/pix.
x 400 pix.
= 1080. Å		2.7 Å/pix.
x 400 pix.
= 1080. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.010900968 - 0.04380354
Average (Standard dev.)0.00078829 (±0.0065251556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 1080.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map

Fileemd_27559_half_map_1.map
AnnotationHalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map

Fileemd_27559_half_map_2.map
AnnotationHalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chikungunya virus strain S27-African prototype

EntireName: Chikungunya virus strain S27-African prototype
Components
  • Virus: Chikungunya virus strain S27-African prototype

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Supramolecule #1: Chikungunya virus strain S27-African prototype

SupramoleculeName: Chikungunya virus strain S27-African prototype / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 371094
Sci species name: Chikungunya virus strain S27-African prototype
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes aegypti (yellow fever mosquito)

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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: 7.5 / Component - Concentration: 1.0 X / Component - Formula: HBS / Component - Name: Hepes Buffer Saline
Details: Hepes Buffer Saline (10mM HEPES, 150mM NaCl, 50mM sodium citrate)
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 495 / Average exposure time: 0.2 sec. / Average electron dose: 43.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7741
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

5580


Details: Low pass filtered to 60A
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5806
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j2w

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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