+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27559 | |||||||||
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Title | Cryo-EM map of Chikungunya virus strain s27 | |||||||||
Map data | Chikungunya virus strain S27 | |||||||||
Sample |
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Biological species | Chikungunya virus strain S27-African prototype | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.75 Å | |||||||||
Authors | Mangala Prasad V / Lee KK | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27559.map.gz | 189.9 MB | EMDB map data format | |
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Header (meta data) | emd-27559-v30.xml emd-27559.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27559_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_27559.png | 222.8 KB | ||
Others | emd_27559_half_map_1.map.gz emd_27559_half_map_2.map.gz | 191 MB 190.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27559 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27559 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27559.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Chikungunya virus strain S27 | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half-map
File | emd_27559_half_map_1.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_27559_half_map_2.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chikungunya virus strain S27-African prototype
Entire | Name: Chikungunya virus strain S27-African prototype |
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Components |
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-Supramolecule #1: Chikungunya virus strain S27-African prototype
Supramolecule | Name: 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 |
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Host (natural) | Organism: Aedes aegypti (yellow fever mosquito) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 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) |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |