|Entry||Database: EMDB / ID: EMD-7890|
|Title||Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2.|
|Sample||Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2. Serum digested and Fab purified before adding trimer.|
|Biological species||Oryctolagus cuniculus (rabbit)|
|Method||single particle reconstruction / negative staining / Resolution: 20 Å|
|Authors||Ward AB / Turner HL|
|Citation||Journal: Immunity / Year: 2018|
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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_7890.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.05 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Negative stain EM map of polyclonal serum in complex with BG505 S...
|Entire||Name: Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2. Serum digested and Fab purified before adding trimer.|
Number of components: 1
-Component #1: protein, Negative stain EM map of polyclonal serum in complex wit...
|Protein||Name: Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2. Serum digested and Fab purified before adding trimer.|
Recombinant expression: No
|Source||Species: Oryctolagus cuniculus (rabbit)|
|Specimen||Specimen state: Particle / Method: negative staining|
|Sample solution||Specimen conc.: 0.063 mg/mL / pH: 7.4|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai Spirit / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI SPIRIT|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: SIDE ENTRY, EUCENTRIC|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 50|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 17487|
|3D reconstruction||Resolution: 20 Å / Resolution method: FSC 0.5 CUT-OFF|
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