+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25024 | |||||||||
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Title | Cryo-EM map for HIV-1 Env bound with one 4E10 Fab | |||||||||
Map data | Cryo-EM map for HIV-1 Env bound with one 4E10 Fab | |||||||||
Sample |
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Biological species | HIV whole-genome vector AA1305#18 (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.79 Å | |||||||||
Authors | Yang S / Walz T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack. Authors: Shuang Yang / Giorgos Hiotis / Yi Wang / Junjian Chen / Jia-Huai Wang / Mikyung Kim / Ellis L Reinherz / Thomas Walz / Abstract: Vaccines targeting HIV-1's gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160's membrane-proximal external region (MPER) is the target of naturally arising ...Vaccines targeting HIV-1's gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160's membrane-proximal external region (MPER) is the target of naturally arising broadly neutralizing antibodies (bnAbs), yet MPER-based vaccines fail to generate bnAbs. Here, nanodisc-embedded spike protein was investigated by cryo-electron microscopy and molecular-dynamics simulations, revealing spontaneous ectodomain tilting that creates vulnerability for HIV-1. While each MPER protomer radiates centrally towards the three-fold axis contributing to a membrane-associated tripod structure that is occluded in the upright spike, tilting provides access to the opposing MPER. Structures of spike proteins with bound 4E10 bnAb Fabs reveal that the antibody binds exposed MPER, thereby altering MPER dynamics, modifying average ectodomain tilt, and imposing strain on the viral membrane and the spike's transmembrane segments, resulting in the abrogation of membrane fusion and informing future vaccine development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25024.map.gz | 57.6 MB | EMDB map data format | |
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Header (meta data) | emd-25024-v30.xml emd-25024.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_25024.png | 67.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25024 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25024 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25024.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map for HIV-1 Env bound with one 4E10 Fab | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : HIV-1 Env with cytoplasmic tail deleted, bound with one 4E10 Fab
Entire | Name: HIV-1 Env with cytoplasmic tail deleted, bound with one 4E10 Fab |
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Components |
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-Supramolecule #1: HIV-1 Env with cytoplasmic tail deleted, bound with one 4E10 Fab
Supramolecule | Name: HIV-1 Env with cytoplasmic tail deleted, bound with one 4E10 Fab type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: HIV whole-genome vector AA1305#18 (others) / Strain: BG505 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23538 |