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Yorodumi- EMDB-23219: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOS... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23219 | |||||||||
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Title | BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) | |||||||||
Map data | BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Main map | |||||||||
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Antanasijevic A / Froes Rocha R / 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_23219.map.gz | 20.4 MB | EMDB map data format | |
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Header (meta data) | emd-23219-v30.xml emd-23219.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23219_fsc.xml | 6.5 KB | Display | FSC data file |
Images | emd_23219.png | 204.3 KB | ||
Masks | emd_23219_msk_1.map | 22.2 MB | Mask map | |
Others | emd_23219_half_map_1.map.gz emd_23219_half_map_2.map.gz | 16.9 MB 16.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23219 | HTTPS FTP |
-Validation report
Summary document | emd_23219_validation.pdf.gz | 705.8 KB | Display | EMDB validaton report |
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Full document | emd_23219_full_validation.pdf.gz | 705.4 KB | Display | |
Data in XML | emd_23219_validation.xml.gz | 12 KB | Display | |
Data in CIF | emd_23219_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23219 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23219 | HTTPS FTP |
-Related structure data
Related structure data | 7l7uMC 7l7tC 7l85C 7l86C 7l87C 7l88C 7l89C 7l8aC 7l8bC 7l8cC 7l8dC 7l8eC 7l8fC 7l8gC 7l8sC 7l8tC 7l8uC 7l8wC 7l8xC 7l8yC 7l8zC 7l90C M: atomic model generated by this map 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_23219.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23219_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: BG505 SOSIP reconstructed from a designed nanoparticle, BG505...
File | emd_23219_half_map_1.map | ||||||||||||
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Annotation | BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BG505 SOSIP reconstructed from a designed nanoparticle, BG505...
File | emd_23219_half_map_2.map | ||||||||||||
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Annotation | BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOS...
Entire | Name: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) |
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Components |
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-Supramolecule #1: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOS...
Supramolecule | Name: BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: The map was generated by subparticle extraction from the BG505 SOSIP-T33-31 nanoparticle using the localized reconstruction approach. |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 / Recombinant plasmid: pPPI4 |
-Macromolecule #1: BG505 SOSIP.v5.2(7S) - gp120
Macromolecule | Name: BG505 SOSIP.v5.2(7S) - gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 56.70748 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHTD IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS ...String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLE NVTEEFNMWK NNMVEQMHTD IISLWDQSLK PCVKLTPLCV TLQCTNVTNN ITDDMRGELK NCSFNMTTEL R DKKQKVYS LFYRLDVVQI NENQGNRSNN SNKEYRLINC NTSAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GP CTNVSTV QCTHGIKPVV STQLLLNGSL AEEEVIIRSE NITNNAKNIL VQLNESVQIN CTRPNNNTVK SIRIGPGQWF YYT GDIIGD IRQAHCNVSK ATWNETLGKV VKQLRKHFGN NTIIRFANSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNT SVQGS NSTGSNDSIT LPCRIKQIIN MWQRIGQAMY APPIQGVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWR SELY KYKVVKIEPL GVAPTRCKRR V |
-Macromolecule #2: BG505 SOSIP.v5.2(7S) - gp41
Macromolecule | Name: BG505 SOSIP.v5.2(7S) - gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 16.543627 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LGFLGAAGST MGAASMTLTV QARNLLSGIV QQQSNLLRAP ECQQHLLKDT HWGIKQLQAR VLAVEHYLRD QQLLGIWGCS GKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLELD |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 39 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.1 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS buffer prepared from a 10X stock | |||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time varied between 3 and 7 seconds.. | |||||||||
Details | BG505 SOSIP-T33-31 nanoparticle was prepared by combining equimolar amounts of BG505 SOSIP-T33-31A and BG505 SOSIP-T33-31B components that were expressed separately. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-41 / Number grids imaged: 2 / Number real images: 1751 / Average exposure time: 10.25 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |