+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24072 | |||||||||
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Title | Ab1245 Fab in complex with BG505 SOSIP.664 and 8ANC195 Fab | |||||||||
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Sample |
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Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Abernathy ME / Bjorkman PJ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: NPJ Vaccines / Year: 2021 Title: Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope. Authors: Morgan E Abernathy / Harry B Gristick / Jost Vielmetter / Jennifer R Keeffe / Priyanthi N P Gnanapragasam / Yu E Lee / Amelia Escolano / Rajeev Gautam / Michael S Seaman / Malcolm A Martin / ...Authors: Morgan E Abernathy / Harry B Gristick / Jost Vielmetter / Jennifer R Keeffe / Priyanthi N P Gnanapragasam / Yu E Lee / Amelia Escolano / Rajeev Gautam / Michael S Seaman / Malcolm A Martin / Michel C Nussenzweig / Pamela J Bjorkman / Abstract: HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. We report ...HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. We report characterization of Ab1245, an off-target antibody against the Env gp120-gp41 interface, from V3-glycan patch immunogen-primed and boosted macaques. A 3.7 Å cryo-EM structure of an Ab1245-Env complex reveals one Ab1245 Fab binding asymmetrically to Env trimer at the gp120-gp41 interface using its long CDRH3 to mimic regions of gp41. The mimicry includes positioning of a CDRH3 methionine into the gp41 tryptophan clasp, resulting in displacement of the fusion peptide and fusion peptide-proximal region. Despite fusion peptide displacement, Ab1245 is non-neutralizing even at high concentrations, raising the possibility that only two fusion peptides per trimer are required for viral-host membrane fusion. These structural analyses facilitate immunogen design to prevent elicitation of Ab1245-like antibodies that block neutralizing antibodies against the fusion peptide. | |||||||||
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_24072.map.gz | 135.4 MB | EMDB map data format | |
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Header (meta data) | emd-24072-v30.xml emd-24072.xml | 29.2 KB 29.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24072_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_24072.png | 138.3 KB | ||
Masks | emd_24072_msk_1.map | 144.7 MB | Mask map | |
Others | emd_24072_additional_1.map.gz emd_24072_half_map_1.map.gz emd_24072_half_map_2.map.gz | 132 MB 35.9 MB 35.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24072 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24072 | HTTPS FTP |
-Validation report
Summary document | emd_24072_validation.pdf.gz | 683.1 KB | Display | EMDB validaton report |
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Full document | emd_24072_full_validation.pdf.gz | 682.7 KB | Display | |
Data in XML | emd_24072_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | emd_24072_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24072 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24072 | HTTPS FTP |
-Related structure data
Related structure data | 7mxeMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24072.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8654 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_24072_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: blurred map
File | emd_24072_additional_1.map | ||||||||||||
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Annotation | blurred map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_24072_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24072_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of NHP-isolated Ab1245 Fab and bNAb 8ANC195 G52K5 Fab bou...
+Supramolecule #1: Complex of NHP-isolated Ab1245 Fab and bNAb 8ANC195 G52K5 Fab bou...
+Supramolecule #2: 8ANC195 G52K5 Fab
+Supramolecule #3: Ab1245 Fab
+Supramolecule #4: BG505 SOSIP.664 trimer
+Macromolecule #1: 8ANC195 G52K5 Fab heavy chain
+Macromolecule #2: 8ANC195 G52K5 Fab light chain
+Macromolecule #3: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41
+Macromolecule #4: Envelope glycoprotein BG505 SOSIP.664 gp120
+Macromolecule #5: Ab1245 Fab heavy chain
+Macromolecule #6: Ab1245 Fab light chain
+Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.7 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: 0 blot force, 3 second blot time, 3 uL sample added. | |||||||||
Details | Ab1245 was incubated with BG505 SOSIP at room temperature for 3 hours, after which 8ANC195 Fab was added and the complex was incubated overnight at RT before SEC purification and concentration to 4.7 mg/mL. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2307 / Average electron dose: 60.0 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: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |