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- EMDB-7554: CryoEM map of BG505 SOSIP.664 in complex with post boost 1 serum ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7554 | |||||||||
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Title | CryoEM map of BG505 SOSIP.664 in complex with post boost 1 serum from rabbit 3417 | |||||||||
![]() | Map of subset classified particles from 3417 Rabbit post boost 1. 3D classified into map with 2 glycan hole antibodies and a hint of density in the trimer base. | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Turner HL / Ward AB / Nogal B | |||||||||
![]() | ![]() Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization. Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner / ![]() ![]() Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.2 KB 11.2 KB | Display Display | ![]() |
Images | ![]() | 55.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78 KB | Display | ![]() |
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Full document | ![]() | 77.1 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7552C ![]() 7553C ![]() 7555C ![]() 7556C ![]() 7557C ![]() 7570C ![]() 7887C ![]() 7888C ![]() 7889C ![]() 7890C ![]() 7891C ![]() 7892C ![]() 7893C ![]() 7894C ![]() 7895C ![]() 7896C ![]() 7903C ![]() 7904C ![]() 7906C ![]() 6cjkC ![]() 6didC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of subset classified particles from 3417 Rabbit post boost 1. 3D classified into map with 2 glycan hole antibodies and a hint of density in the trimer base. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of BG505 SOSIP.664 and serum antibodies from post boost 1...
Entire | Name: Complex of BG505 SOSIP.664 and serum antibodies from post boost 1 from rabbit 3417. |
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Components |
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-Supramolecule #1: Complex of BG505 SOSIP.664 and serum antibodies from post boost 1...
Supramolecule | Name: Complex of BG505 SOSIP.664 and serum antibodies from post boost 1 from rabbit 3417. type: complex / ID: 1 / Parent: 0 Details: Serum was purified through SEC after using a Protein A or G column to capture complex then cleave IgG releasing Fab and trimer. Substoichiometric occupancy and flexibility show lack of ...Details: Serum was purified through SEC after using a Protein A or G column to capture complex then cleave IgG releasing Fab and trimer. Substoichiometric occupancy and flexibility show lack of density in Fab region while trimer core is refined to higher resolution. Map shows two strong densities of glycan hole Fab and a hint of Fab at the trimer base. |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.44 mg/mL |
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Buffer | pH: 7.4 / Details: TBS |
Grid | Model: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | Sample in TBS, added 0.5uL of DDM at 0.42mM. Sample was monodisperse |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-46 / Average exposure time: 11.5 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |