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- EMDB-7889: Negative Stain EM map of polyclonal serum in complex with BG505 S... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7889 | |||||||||
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Title | Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2. | |||||||||
![]() | Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2 | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
![]() | Ward AB / Turner HL | |||||||||
![]() | ![]() 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 | ![]() | 6.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11 KB 11 KB | Display Display | ![]() |
Images | ![]() | 62.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7552C ![]() 7553C ![]() 7554C ![]() 7555C ![]() 7556C ![]() 7557C ![]() 7570C ![]() 7887C ![]() 7888C ![]() 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 | Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from rabbit 3419 at post boost 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 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 : 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. |
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Components |
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-Supramolecule #1: Negative stain EM map of polyclonal serum in complex with BG505 S...
Supramolecule | 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. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.063 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: TBS |
Staining | Type: NEGATIVE / Material: Uranyl formate |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CELLULOSE ACETATE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 50 / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | ![]() Model: Tecnai Spirit / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 17487 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1) |
Final 3D classification | Software - Name: RELION (ver. 2.1) |