+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22527 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Icosahedral Map of ZIKV MR-766 | |||||||||
Map data | Icosahedral Map of ZIKV MR-766 | |||||||||
Sample |
| |||||||||
Biological species | Zika virus | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å | |||||||||
Authors | Jose J / Hafenstein S | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Identification of a pocket factor that is critical to Zika virus assembly. Authors: Nadia M DiNunno / Daniel J Goetschius / Anoop Narayanan / Sydney A Majowicz / Ibrahim Moustafa / Carol M Bator / Susan L Hafenstein / Joyce Jose / Abstract: Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an ...Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an atomic resolution structure is challenging, but important to understand virus assembly and life cycle mechanisms that offer distinct targets for therapeutic intervention. We here use subvolume refinement to achieve a 3.4 Å resolution structure and identify two distinct lipid moieties. The first arises from the inner leaflet and is coordinated by hydrophobic residues of the M and E transmembrane helices that form a binding pocket not previously characterized. The second lipid arises from the outer leaflet coordinate between two E protein helices. Structure-based mutagenesis identifies critical hydrophobic interactions and their effect on the virus life cycle. Results show that lipids play an essential role in the ZIKV assembly pathway revealing a potential target of lipid based antiviral drug development. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22527.map.gz | 1 GB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-22527-v30.xml emd-22527.xml | 8 KB 8 KB | Display Display | EMDB header |
Images | emd_22527.png | 239.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22527 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22527 | HTTPS FTP |
-Validation report
Summary document | emd_22527_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_22527_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_22527_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22527 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22527 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_22527.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Icosahedral Map of ZIKV MR-766 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Zika virus
Entire | Name: Zika virus |
---|---|
Components |
|
-Supramolecule #1: Zika virus
Supramolecule | Name: Zika virus / type: virus / ID: 1 / Parent: 0 / Details: propagated in HeLa cells / NCBI-ID: 64320 / Sci species name: Zika virus / Sci species strain: MR-766 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: mosquito (mosquito) |
Virus shell | Shell ID: 1 / Name: Zika / Diameter: 50.0 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
---|---|
Buffer | pH: 7 |
Staining | Type: NEGATIVE / Material: PTA |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 41.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9100 |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |