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Yorodumi- EMDB-41631: Cryo-EM structure of Chikungunya virus with asymmetric reconstruction -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41631 | |||||||||
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Title | Cryo-EM structure of Chikungunya virus with asymmetric reconstruction | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Chikungunya virus / VIRUS | |||||||||
Biological species | Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | Su GC / Chmielewsk D / Kaelber J / Pintilie G / Chen M / Jin J / Auguste A / Chiu W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: PNAS Nexus / Year: 2024 Title: Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses. Authors: David Chmielewski / Guan-Chin Su / Jason T Kaelber / Grigore D Pintilie / Muyuan Chen / Jing Jin / Albert J Auguste / Wah Chiu / Abstract: Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) ...Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) reconstructions, which impose icosahedral symmetry on the viral particles. Using cryogenic electron tomography (cryo-ET), we revealed a polarized symmetry defect in the icosahedral lattice of Chikungunya virus (CHIKV) in situ, similar to the late budding particles, suggesting the inherent imperfect symmetry originates from the final pinch-off of assembled virions. We further demonstrated this imperfect symmetry is also present in in vitro purified CHIKV and Mayaro virus, another arthritogenic alphavirus. We employed a subparticle-based single-particle analysis protocol to circumvent the icosahedral imperfection and boosted the resolution of the structure of the CHIKV to ∼3 Å resolution, which revealed detailed molecular interactions between glycoprotein E1-E2 heterodimers in the transmembrane region and multiple lipid-like pocket factors located in a highly conserved hydrophobic pocket. This complementary use of in situ cryo-ET and single-particle cryo-EM approaches provides a more precise structural description of near-icosahedral viruses and valuable insights to guide the development of structure-based antiviral therapies against alphaviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41631.map.gz | 47.7 MB | EMDB map data format | |
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Header (meta data) | emd-41631-v30.xml emd-41631.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41631_fsc.xml | 12.4 KB | Display | FSC data file |
Images | emd_41631.png | 109.4 KB | ||
Filedesc metadata | emd-41631.cif.gz | 4.5 KB | ||
Others | emd_41631_half_map_1.map.gz emd_41631_half_map_2.map.gz | 129.1 MB 128.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41631 | HTTPS FTP |
-Validation report
Summary document | emd_41631_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_41631_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_41631_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_41631_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41631 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41631.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.68 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41631_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41631_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chikungunya virus
Entire | Name: Chikungunya virus |
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Components |
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-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: vaccine strain 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Molecular weight | Theoretical: 500 KDa |
Virus shell | Shell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Average electron dose: 47.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 106000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |