+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9692 | |||||||||
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Title | Cryo-EM structure of alphavirus capsid | |||||||||
Map data | Cryo-EM structure of alphavirus capsid | |||||||||
Sample |
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Biological species | Sindbis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Zhang X / Chen L / Wang M / Zhu D / Sun Z | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure. Authors: Lihong Chen / Ming Wang / Dongjie Zhu / Zhenzhao Sun / Jun Ma / Jinglin Wang / Lingfei Kong / Shida Wang / Zaisi Liu / Lili Wei / Yuwen He / Jingfei Wang / Xinzheng Zhang / Abstract: Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. ...Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9692.map.gz | 81 MB | EMDB map data format | |
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Header (meta data) | emd-9692-v30.xml emd-9692.xml | 7.5 KB 7.5 KB | Display Display | EMDB header |
Images | emd_9692.png | 282.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9692 | HTTPS FTP |
-Validation report
Summary document | emd_9692_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_9692_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_9692_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9692 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9692.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of alphavirus capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Sindbis virus
Entire | Name: Sindbis virus |
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Components |
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-Supramolecule #1: Sindbis virus
Supramolecule | Name: Sindbis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29974 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |