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Yorodumi- EMDB-23186: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23186 | |||||||||
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Title | BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B | |||||||||
Map data | BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.6 Å | |||||||||
Authors | Antanasijevic A / Sewall LM / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Authors: Aleksandar Antanasijevic / Leigh M Sewall / Christopher A Cottrell / Diane G Carnathan / Luis E Jimenez / Julia T Ngo / Jennifer B Silverman / Bettina Groschel / Erik Georgeson / Jinal ...Authors: Aleksandar Antanasijevic / Leigh M Sewall / Christopher A Cottrell / Diane G Carnathan / Luis E Jimenez / Julia T Ngo / Jennifer B Silverman / Bettina Groschel / Erik Georgeson / Jinal Bhiman / Raiza Bastidas / Celia LaBranche / Joel D Allen / Jeffrey Copps / Hailee R Perrett / Kimmo Rantalainen / Fabien Cannac / Yuhe R Yang / Alba Torrents de la Peña / Rebeca Froes Rocha / Zachary T Berndsen / David Baker / Neil P King / Rogier W Sanders / John P Moore / Shane Crotty / Max Crispin / David C Montefiori / Dennis R Burton / William R Schief / Guido Silvestri / Andrew B Ward / Abstract: Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate ...Engineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic. | |||||||||
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_23186.map.gz | 11.7 MB | EMDB map data format | |
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Header (meta data) | emd-23186-v30.xml emd-23186.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
Images | emd_23186.png | 35.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23186 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23186 | HTTPS FTP |
-Related structure data
Related structure data | 7l7tC 7l7uC 7l85C 7l86C 7l87C 7l88C 7l89C 7l8aC 7l8bC 7l8cC 7l8dC 7l8eC 7l8fC 7l8gC 7l8sC 7l8tC 7l8uC 7l8wC 7l8xC 7l8yC 7l8zC 7l90C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23186.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B
Entire | Name: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B |
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Components |
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-Supramolecule #1: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B
Supramolecule | Name: BG505 SOSIP fused to a trimeric nanoparticle building block, T33-31B type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Genetic fusion, recombinantly expressed and purified |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pPPI4 |
-Macromolecule #1: BG505 SOSIP-T33-31B
Macromolecule | Name: BG505 SOSIP-T33-31B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF ...String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CTNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVIIRSENIT NNAKNILVQL NESVQINCTR PNNNTVKSIR IGPGQWFYYT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAVGIGAV SLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PECQQHLLKD THWGIKQLQA RVLAVEHYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLELDGSGS GSGSGSVRGI RGAITVEEDT PAAILAATIE LLLKMLEANG IQSYEELAAV IFTVTEDLTS AFPAEAARLI GMHRVPLLSA REVPVPGSLP RVIRVLALWN TDTPQDRVRH VYLNEAVRLR PDLESAQLE |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS buffer, pH 7.4 | |||||||||
Staining | Type: NEGATIVE / Material: Uranyl Formate Details: Sample diluted to 0.05 mg/mL. 3 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 60 seconds. | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Details | Antigen-bearing component was expressed in HEK293 cells and purified using PGT145 column. |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Particle selection | Details: Appion manual picker |
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Startup model | Type of model: OTHER Details: Negative stain EM map of the free BG505 SOSIP trimer |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final 3D classification | Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 29784 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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