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Yorodumi- EMDB-21411: HIV envelope glycoprotein bound with soluble CD4 (D1-D2) and anti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21411 | |||||||||
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Title | HIV envelope glycoprotein bound with soluble CD4 (D1-D2) and antibody 17b on AT-2 treated BaL strain virus | |||||||||
Map data | HIV envelope glycoprotein bound with soluble CD4 (D1-D2) and antibody 17b on AT-2 treated BaL strain virus | |||||||||
Sample |
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Biological species | Human immunodeficiency virus 1 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.7 Å | |||||||||
Authors | Jun L / Ze L / Li W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles. Authors: Ze Li / Wenwei Li / Maolin Lu / Julian Bess / Cara W Chao / Jason Gorman / Daniel S Terry / Baoshan Zhang / Tongqing Zhou / Scott C Blanchard / Peter D Kwong / Jeffrey D Lifson / Walther Mothes / Jun Liu / Abstract: The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env ...The HIV-1 envelope glycoprotein (Env) trimer, composed of gp120 and gp41 subunits, mediates viral entry into cells. Recombinant Env trimers have been studied structurally, but characterization of Env embedded in intact virus membranes has been limited to low resolution. Here, we deploy cryo-electron tomography and subtomogram averaging to determine the structures of Env trimers on aldrithiol-2 (AT-2)-inactivated virions in ligand-free, antibody-bound and CD4-bound forms at subnanometer resolution. Tomographic reconstructions document molecular features consistent with high-resolution structures of engineered soluble and detergent-solubilized Env trimers. One of three conformational states previously predicted by smFRET was not observed by cryo-ET, potentially owing to AT-2 inactivation. We did observe Env trimers to open in situ in response to CD4 binding, with an outward movement of gp120-variable loops and an extension of a critical gp41 helix. Overall features of Env trimer embedded in AT-2-treated virions appear well-represented by current engineered trimers. | |||||||||
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_21411.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-21411-v30.xml emd-21411.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_21411.png | 111.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21411 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21411 | HTTPS FTP |
-Validation report
Summary document | emd_21411_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_21411_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_21411_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21411 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21411 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21411.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV envelope glycoprotein bound with soluble CD4 (D1-D2) and antibody 17b on AT-2 treated BaL strain virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : HIV gp120-gp41 trimer
Entire | Name: HIV gp120-gp41 trimer |
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Components |
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-Supramolecule #1: HIV gp120-gp41 trimer
Supramolecule | Name: HIV gp120-gp41 trimer / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: BaL strain |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Number subtomograms used: 13817 |
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Extraction | Number tomograms: 208 / Number images used: 15353 |
Final angle assignment | Type: OTHER |