[English] 日本語
Yorodumi- EMDB-27603: BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 base, N335/N289, V1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27603 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 base, N335/N289, V1/V3 and V5/C3 epitope pAbs | |||||||||
Map data | Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (main map) | |||||||||
Sample |
| |||||||||
Keywords | polyclonal antibodies / HIV-1 / Env / non-human primate / VIRAL PROTEIN | |||||||||
Biological species | Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Sewall LM / Richey ST / Ozorowski G / Ward AB | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Nature / Year: 2022 Title: Long-primed germinal centres with enduring affinity maturation and clonal migration. Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L ...Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L Torres / Wen-Hsin Lee / Erik Georgeson / Michael Kubitz / Sam Hodges / Tina-Marie Mullen / Yumiko Adachi / Kimberly M Cirelli / Amitinder Kaur / Carolina Allers / Marissa Fahlberg / Brooke F Grasperge / Jason P Dufour / Faith Schiro / Pyone P Aye / Oleksandr Kalyuzhniy / Alessia Liguori / Diane G Carnathan / Guido Silvestri / Xiaoying Shen / David C Montefiori / Ronald S Veazey / Andrew B Ward / Lars Hangartner / Dennis R Burton / Darrell J Irvine / William R Schief / Shane Crotty / Abstract: Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further ...Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (B) cells that last for at least 6 months. A 186-fold increase in B cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of B cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding B cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous B cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27603.map.gz | 20.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27603-v30.xml emd-27603.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_27603.png | 52.9 KB | ||
Filedesc metadata | emd-27603.cif.gz | 4.5 KB | ||
Others | emd_27603_additional_1.map.gz emd_27603_half_map_1.map.gz emd_27603_half_map_2.map.gz | 8.3 MB 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27603 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27603 | HTTPS FTP |
-Validation report
Summary document | emd_27603_validation.pdf.gz | 736.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_27603_full_validation.pdf.gz | 735.7 KB | Display | |
Data in XML | emd_27603_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_27603_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27603 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27603 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_27603.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (main map) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Rh.DGT5 wk13 base and V5/C3 pAbs (additional map 1)
File | emd_27603_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Rh.DGT5 wk13 base and V5/C3 pAbs (additional map 1) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (half map 1)
File | emd_27603_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (half map 1) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (half map 2)
File | emd_27603_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Rh.DGT5 wk13 N335/N289 and V1V3 pAbs (half map 2) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 N335/N289 and V1/V3...
Entire | Name: BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 N335/N289 and V1/V3 epitope pAbs |
---|---|
Components |
|
-Supramolecule #1: BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 N335/N289 and V1/V3...
Supramolecule | Name: BG505 MD39 SOSIP in complex with Rh.DGT5 wk13 N335/N289 and V1/V3 epitope pAbs type: complex / ID: 1 / Parent: 0 |
---|
-Supramolecule #2: Rh.DGT5 wk13 N335/N289 and V1/V3 epitope pAbs
Supramolecule | Name: Rh.DGT5 wk13 N335/N289 and V1/V3 epitope pAbs / type: complex / ID: 2 / Parent: 1 |
---|---|
Source (natural) | Organism: Macaca mulatta (Rhesus monkey) |
-Supramolecule #3: BG505 MD39 SOSIP
Supramolecule | Name: BG505 MD39 SOSIP / type: complex / ID: 3 / Parent: 1 |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
---|---|
Buffer | pH: 7.4 |
Staining | Type: NEGATIVE / Material: Uranyl formate |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 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: 1.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2991 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |