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Yorodumi- EMDB-0570: HIV-1 vaccine elicited polyclonal 99-13 Fab in complex with the H... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0570 | |||||||||
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Title | HIV-1 vaccine elicited polyclonal 99-13 Fab in complex with the HIV Env trimer BG505 SOSIPv5.2 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / Macaca (macaques) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.5 Å | |||||||||
Authors | Nogal B / Ward AB | |||||||||
Citation | Journal: Cell / Year: 2019 Title: Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Authors: Kimberly M Cirelli / Diane G Carnathan / Bartek Nogal / Jacob T Martin / Oscar L Rodriguez / Amit A Upadhyay / Chiamaka A Enemuo / Etse H Gebru / Yury Choe / Federico Viviano / Catherine ...Authors: Kimberly M Cirelli / Diane G Carnathan / Bartek Nogal / Jacob T Martin / Oscar L Rodriguez / Amit A Upadhyay / Chiamaka A Enemuo / Etse H Gebru / Yury Choe / Federico Viviano / Catherine Nakao / Matthias G Pauthner / Samantha Reiss / Christopher A Cottrell / Melissa L Smith / Raiza Bastidas / William Gibson / Amber N Wolabaugh / Mariane B Melo / Benjamin Cossette / Venkatesh Kumar / Nirav B Patel / Talar Tokatlian / Sergey Menis / Daniel W Kulp / Dennis R Burton / Ben Murrell / William R Schief / Steven E Bosinger / Andrew B Ward / Corey T Watson / Guido Silvestri / Darrell J Irvine / Shane Crotty / Abstract: Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the ...Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (T) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes. | |||||||||
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_0570.map.gz | 6.3 MB | EMDB map data format | |
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Header (meta data) | emd-0570-v30.xml emd-0570.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_0570.png | 48.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0570 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0570 | HTTPS FTP |
-Validation report
Summary document | emd_0570_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_0570_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_0570_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0570 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0570 | HTTPS FTP |
-Related structure data
Related structure data | 0569C 0571C 0572C 0573C 0574C 0575C 0576C 0577C 0578C 0579C 0580C 0581C 0582C 9138C 9175C 9176C 9177C 9178C 9179C 9180C 9181C 9182C 9183C 9184C 9185C 9186C 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_0570.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : HIV-1 vaccine elicited Fab in complex with the HIV Env trimer BG5...
Entire | Name: HIV-1 vaccine elicited Fab in complex with the HIV Env trimer BG505 SOSIPv5.2 |
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Components |
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-Supramolecule #1: HIV-1 vaccine elicited Fab in complex with the HIV Env trimer BG5...
Supramolecule | Name: HIV-1 vaccine elicited Fab in complex with the HIV Env trimer BG505 SOSIPv5.2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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-Supramolecule #2: SOSIP trimer
Supramolecule | Name: SOSIP trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Polyclonal Fab
Supramolecule | Name: Polyclonal Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: Macaca (macaques) |
-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 12 |
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Image recording | Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |