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- EMDB-23225: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from a... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23225 | |||||||||
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Title | BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point) | |||||||||
![]() | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point). Main map | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Antanasijevic A / Sewall LM / Cannac F / Perrett HR / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 165.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.6 KB 27.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 169 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Others | ![]() ![]() | 140.5 MB 140.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l88MC ![]() 7l7tC ![]() 7l7uC ![]() 7l85C ![]() 7l86C ![]() 7l87C ![]() 7l89C ![]() 7l8aC ![]() 7l8bC ![]() 7l8cC ![]() 7l8dC ![]() 7l8eC ![]() 7l8fC ![]() 7l8gC ![]() 7l8sC ![]() 7l8tC ![]() 7l8uC ![]() 7l8wC ![]() 7l8xC ![]() 7l8yC ![]() 7l8zC ![]() 7l90C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point). Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23225_half_map_1.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point). Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 3D map of BG505 SOSIP MD39 in complex...
File | emd_23225_half_map_2.map | ||||||||||||
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Annotation | 3D map of BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point). Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from a...
Entire | Name: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point) |
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Components |
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-Supramolecule #1: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from a...
Supramolecule | Name: BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from ...Details: Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from the immune complex dataset using the focused classification approach. |
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-Supramolecule #2: BG505 SOSIP MD39 gp120/gp41
Supramolecule | Name: BG505 SOSIP MD39 gp120/gp41 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: polyclonal Fab pAbC-3 from animal Rh.32034
Supramolecule | Name: polyclonal Fab pAbC-3 from animal Rh.32034 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-Macromolecule #1: BG505 SOSIP MD39 - gp120
Macromolecule | Name: BG505 SOSIP MD39 - gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 55.520109 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGILPSPGMP ALLSLVSLLM GCVAETGAEN LWVTVYYGVP VWKDAETTLF CASDAKAYET KKHNVWATHC CVPTDPNPQE IHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ K VYSLFYRL ...String: MGILPSPGMP ALLSLVSLLM GCVAETGAEN LWVTVYYGVP VWKDAETTLF CASDAKAYET KKHNVWATHC CVPTDPNPQE IHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ K VYSLFYRL DVVQINENQG NRSNNSNKEY RLINCNTSAI TQACPKVSFE PIPIHYCAPA GFAILKCKDK KFNGTGPCPS VS TVQCTHG IKPVVSTQLL LNGSLAEEEV IIRSENITNN AKNILVQLNT PVQINCTRPN NNTVKSIRIG PGQWFYYTGD IIG DIRQAH CNVSKATWNE TLGKVVKQLR KHFGNNTIIR FAQSSGGDLE VTTHSFNCGG EFFYCNTSGL FNSTWISNTS VQGS NSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYK YKVV KIEPLGVAPT RCKR |
-Macromolecule #2: BG505 SOSIP MD39 - gp41
Macromolecule | Name: BG505 SOSIP MD39 - gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 16.57074 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PECQQHLLKL THWGIKQLQA RVLAVEHYLR DQQLLGIWGC SGKLICCTN VPWNSSWSNR NLSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD |
-Macromolecule #3: Rh.32034 pAbC-3 - Heavy Chain
Macromolecule | Name: Rh.32034 pAbC-3 - Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 9.719973 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK) |
-Macromolecule #4: Rh.32034 pAbC-3 - Light Chain
Macromolecule | Name: Rh.32034 pAbC-3 - Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 9.124238 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 27 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS buffer prepared from a 10X stock | |||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / 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 | Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 2 / Number real images: 3194 / Average exposure time: 7.5 sec. / Average electron dose: 44.9 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |