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Yorodumi- EMDB-7554: CryoEM map of BG505 SOSIP.664 in complex with post boost 1 serum ... -
+Open data
-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 data | 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. | |||||||||
Sample |
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Biological species | Human immunodeficiency virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
Authors | Turner HL / Ward AB / Nogal B | |||||||||
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. | |||||||||
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_7554.map.gz | 96.5 MB | EMDB map data format | |
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Header (meta data) | emd-7554-v30.xml emd-7554.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_7554.png | 55.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7554 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7554 | 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 (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7554.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: Human immunodeficiency virus |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Details: DogPicker was used to pick particles from micrographs |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 0.6.3) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.6.3) / Number images used: 28432 |