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Yorodumi- EMDB-23175: nsEM maps of BG505 SOSIP MD39 in complex with the polyclonal Fab ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23175 | |||||||||
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Title | nsEM maps of BG505 SOSIP MD39 in complex with the polyclonal Fab samples from Group 1 of immunized rhesus macaques (Animal IDs: Rh.32034, Rh.32113, Rh.33104, Rh.33395, Rh.34909, Rh.34943) | |||||||||
Map data | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.34943. Obtained through negative stain EM. | |||||||||
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 / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Antanasijevic A / Sewall LM / Ward A | |||||||||
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_23175.map.gz | 20.6 MB | EMDB map data format | |
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Header (meta data) | emd-23175-v30.xml emd-23175.xml | 26.3 KB 26.3 KB | Display Display | EMDB header |
Images | emd_23175.png | 40.3 KB | ||
Others | emd_23175_additional_1.map.gz emd_23175_additional_2.map.gz emd_23175_additional_3.map.gz emd_23175_additional_4.map.gz emd_23175_additional_5.map.gz | 20.7 MB 20.6 MB 20.6 MB 20.6 MB 20.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23175 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23175 | HTTPS FTP |
-Validation report
Summary document | emd_23175_validation.pdf.gz | 328.9 KB | Display | EMDB validaton report |
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Full document | emd_23175_full_validation.pdf.gz | 328.4 KB | Display | |
Data in XML | emd_23175_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_23175_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23175 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23175 | 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_23175.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.34943. Obtained through negative stain EM. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Additional map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23175_additional_1.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.34909. Obtained through negative stain EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23175_additional_2.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.33395. Obtained through negative stain EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23175_additional_3.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.33104. Obtained through negative stain EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23175_additional_4.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.32113. Obtained through negative stain EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23175_additional_5.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab sample from animal Rh.32034. Obtained through negative stain EM. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BG505 SOSIP MD39 in complex with the polyclonal Fab samples from ...
Entire | Name: BG505 SOSIP MD39 in complex with the polyclonal Fab samples from Group 1 of immunized rhesus macaques (Animal IDs: Rh.32034, Rh.32113, Rh.33104, Rh.33395, Rh.34909, Rh.34943) |
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Components |
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-Supramolecule #1: BG505 SOSIP MD39 in complex with the polyclonal Fab samples from ...
Supramolecule | Name: BG505 SOSIP MD39 in complex with the polyclonal Fab samples from Group 1 of immunized rhesus macaques (Animal IDs: Rh.32034, Rh.32113, Rh.33104, Rh.33395, Rh.34909, Rh.34943) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. |
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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 MD39
Macromolecule | Name: BG505 SOSIP MD39 / 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 KAYETEKHNV WATHACVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF ...String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETEKHNV WATHACVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHEDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT SAITQACPKV SFEPIPIHYC APAGWAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVIIRSENIT NNAKNILVQF NTPVQINCTR PNNNTVKSIR IGPGQAFYYT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFAQSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAVGIGAV SLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PEPQQHLLKD THWGIKQLQA RVLAVEHYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLALD |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 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 | Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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