|Entry||Database: EMDB / ID: EMD-9175|
|Title||Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from non-human primate 224-13|
|Sample||Negative Stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from non-human primate 224-13|
|Biological species||Macaca (macaques)|
|Method||single particle reconstruction / Resolution: 26.8 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 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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9175.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 non-human primate 224-13|
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 non-human primate 224-13|
Recombinant expression: No
|Source||Species: Macaca (macaques)|
|Specimen||Specimen state: Particle|
|Sample solution||pH: 7.5|
|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: OTHER|
|Camera||Detector: FEI EAGLE (2k x 2k)|
|Processing||Method: single particle reconstruction / Number of projections: 4480|
|3D reconstruction||Software: RELION / Resolution: 26.8 Å / Resolution method: FSC 0.143 CUT-OFF|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi