+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15763 | |||||||||
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Title | Untreatment WT HIV-1 immature gag | |||||||||
Map data | merged map | |||||||||
Sample |
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Keywords | HIV / immature / gag / untreatment / VIRUS LIKE PARTICLE | |||||||||
Biological species | HIV-1 06TG.HT038 (virus) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Waheed AA / Zhu Y / Agostino E / Naing L / Soheilian F / Song Y / Zhang P / Yoo S / Shlusher SB / Haughey N / Freed OE | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Neutral sphingomyelinase 2 is required for HIV-1 maturation. Authors: Abdul A Waheed / Yanan Zhu / Eva Agostino / Lwar Naing / Yuta Hikichi / Ferri Soheilian / Seung-Wan Yoo / Yun Song / Peijun Zhang / Barbara S Slusher / Norman J Haughey / Eric O Freed / Abstract: HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the ...HIV-1 assembly occurs at the inner leaflet of the plasma membrane (PM) in highly ordered membrane microdomains. The size and stability of membrane microdomains is regulated by activity of the sphingomyelin hydrolase neutral sphingomyelinase 2 (nSMase2) that is localized primarily to the inner leaflet of the PM. In this study, we demonstrate that pharmacological inhibition or depletion of nSMase2 in HIV-1-producer cells results in a block in the processing of the major viral structural polyprotein Gag and the production of morphologically aberrant, immature HIV-1 particles with severely impaired infectivity. We find that disruption of nSMase2 also severely inhibits the maturation and infectivity of other primate lentiviruses HIV-2 and simian immunodeficiency virus, has a modest or no effect on nonprimate lentiviruses equine infectious anemia virus and feline immunodeficiency virus, and has no effect on the gammaretrovirus murine leukemia virus. These studies demonstrate a key role for nSMase2 in HIV-1 particle morphogenesis and maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15763.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-15763-v30.xml emd-15763.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_15763.png | 91.5 KB | ||
Filedesc metadata | emd-15763.cif.gz | 3.9 KB | ||
Others | emd_15763_half_map_1.map.gz emd_15763_half_map_2.map.gz | 36.3 MB 36.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15763 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15763 | HTTPS FTP |
-Validation report
Summary document | emd_15763_validation.pdf.gz | 863.1 KB | Display | EMDB validaton report |
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Full document | emd_15763_full_validation.pdf.gz | 862.7 KB | Display | |
Data in XML | emd_15763_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_15763_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15763 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15763 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15763.map.gz / Format: CCP4 / Size: 40.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | merged map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half1
File | emd_15763_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_15763_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HIV-1 06TG.HT038
Entire | Name: HIV-1 06TG.HT038 (virus) |
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Components |
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-Supramolecule #1: HIV-1 06TG.HT038
Supramolecule | Name: HIV-1 06TG.HT038 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 587209 / Sci species name: HIV-1 06TG.HT038 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 119237 |
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Extraction | Number tomograms: 45 / Number images used: 119237 |
Final angle assignment | Type: ANGULAR RECONSTITUTION |