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Yorodumi- EMDB-27038: N332-GT2 trimer in complex with pooled polyclonal fab from BG18-e... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27038 | |||||||||||||||
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Title | N332-GT2 trimer in complex with pooled polyclonal fab from BG18-exposed mice (day 42) | |||||||||||||||
Map data | refined map of N332-GT2 trimer in complex with pooled polyclonal fab from BG18-exposed mice (day 42) | |||||||||||||||
Sample |
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Biological species | Human immunodeficiency virus / Mus musculus (house mouse) | |||||||||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||||||||
Authors | Jackson AM / Nogal B / Ward AB | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Immunity / Year: 2022 Title: Antibodies from primary humoral responses modulate the recruitment of naive B cells during secondary responses. Authors: Jeroen M J Tas / Ja-Hyun Koo / Ying-Cing Lin / Zhenfei Xie / Jon M Steichen / Abigail M Jackson / Blake M Hauser / Xuesong Wang / Christopher A Cottrell / Jonathan L Torres / John E Warner / ...Authors: Jeroen M J Tas / Ja-Hyun Koo / Ying-Cing Lin / Zhenfei Xie / Jon M Steichen / Abigail M Jackson / Blake M Hauser / Xuesong Wang / Christopher A Cottrell / Jonathan L Torres / John E Warner / Kathrin H Kirsch / Stephanie R Weldon / Bettina Groschel / Bartek Nogal / Gabriel Ozorowski / Sandhya Bangaru / Nicole Phelps / Yumiko Adachi / Saman Eskandarzadeh / Michael Kubitz / Dennis R Burton / Daniel Lingwood / Aaron G Schmidt / Usha Nair / Andrew B Ward / William R Schief / Facundo D Batista / Abstract: Vaccines generate high-affinity antibodies by recruiting antigen-specific B cells to germinal centers (GCs), but the mechanisms governing the recruitment to GCs on secondary challenges remain unclear. ...Vaccines generate high-affinity antibodies by recruiting antigen-specific B cells to germinal centers (GCs), but the mechanisms governing the recruitment to GCs on secondary challenges remain unclear. Here, using preclinical SARS-CoV and HIV mouse models, we demonstrated that the antibodies elicited during primary humoral responses shaped the naive B cell recruitment to GCs during secondary exposures. The antibodies from primary responses could either enhance or, conversely, restrict the GC participation of naive B cells: broad-binding, low-affinity, and low-titer antibodies enhanced recruitment, whereas, by contrast, the high titers of high-affinity, mono-epitope-specific antibodies attenuated cognate naive B cell recruitment. Thus, the directionality and intensity of that effect was determined by antibody concentration, affinity, and epitope specificity. Circulating antibodies can, therefore, be important determinants of antigen immunogenicity. Future vaccines may need to overcome-or could, alternatively, leverage-the effects of circulating primary antibodies on subsequent naive B cell recruitment. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27038.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-27038-v30.xml emd-27038.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_27038.png | 15.9 KB | ||
Others | emd_27038_half_map_1.map.gz emd_27038_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27038 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27038 | HTTPS FTP |
-Validation report
Summary document | emd_27038_validation.pdf.gz | 492.1 KB | Display | EMDB validaton report |
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Full document | emd_27038_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | emd_27038_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_27038_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27038 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27038 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27038.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | refined map of N332-GT2 trimer in complex with pooled polyclonal fab from BG18-exposed mice (day 42) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map of N332-GT2 trimer in complex with...
File | emd_27038_half_map_1.map | ||||||||||||
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Annotation | half map of N332-GT2 trimer in complex with pooled polyclonal fab from BG18-exposed mice (day 42) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of N332-GT2 trimer in complex with...
File | emd_27038_half_map_2.map | ||||||||||||
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Annotation | half map of N332-GT2 trimer in complex with pooled polyclonal fab from BG18-exposed mice (day 42) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : N332-GT2 trimer in complex with pooled polyclonal fab from wild t...
Entire | Name: N332-GT2 trimer in complex with pooled polyclonal fab from wild type mice (d42) |
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Components |
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-Supramolecule #1: N332-GT2 trimer in complex with pooled polyclonal fab from wild t...
Supramolecule | Name: N332-GT2 trimer in complex with pooled polyclonal fab from wild type mice (d42) type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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-Supramolecule #2: N332-GT2 trimer
Supramolecule | Name: N332-GT2 trimer / type: complex / Chimera: Yes / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Human immunodeficiency virus |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: pooled polyclonal fab from BG18-exposed mice (d42)
Supramolecule | Name: pooled polyclonal fab from BG18-exposed mice (d42) / type: complex / Chimera: Yes / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: uranyl formate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 76912 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |