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- EMDB-43910: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B... -
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Open data
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Basic information
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Title | nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474) | |||||||||
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![]() | HIV / Polyclonal / Antibodies / nsEMPEM / Rabbit / VIRAL PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
![]() | Brown S / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens. Authors: Sharidan Brown / Aleksandar Antanasijevic / Leigh M Sewall / Daniel Montiel Garcia / James Ferguson / Philip J M Brouwer / Rogier W Sanders / Andrew B Ward / ![]() ![]() ![]() Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody ...Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 33.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
Images | ![]() | 439.6 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 33.1 MB 33.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 703.6 KB | Display | ![]() |
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Full document | ![]() | 703.2 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43910_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43910_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B...
Entire | Name: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474) |
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Components |
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-Supramolecule #1: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B...
Supramolecule | Name: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Rabbit Polyclonal Antibody - Base Epitope
Supramolecule | Name: Rabbit Polyclonal Antibody - Base Epitope / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: HIV-1 CH505/BG505 SOSIP.v8.1 Env
Supramolecule | Name: HIV-1 CH505/BG505 SOSIP.v8.1 Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 Details: Chimeric antigen composed of CH505 and BG505 HIV-1 strains. |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140
Macromolecule | Name: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140 / type: protein_or_peptide / ID: 1 Details: The sequence contains engineered SOSIP mutations. This is a chimeric antigen composed of CH505 and BG505 HIV-1 strains. Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK RNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK RNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA LFYKLDIVQL DGNSSQYRLI NCNTSAITQA CPKVSFEPIP IHYCAPAGFA ILKCNNKTFT GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEGEIIIRS ENITNNVKTI LVHLNESVKI ECTRPNNKTV TSIRIGPGQW FYAYGQVIGD IREAYCNINE STWNETLGKV VKQLRKHFGN NTIIRFQPSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRVGQAMYA PPIQGVIRCV SNITGLILTR DGGKNNTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRCKRRVVGR RRRRRAVGIG AVSLGFLGAA GSTMGAASMT LTVQARNLLS GIVQQQSNLL RAPECQQHLL KDTHWGIKQL QARVLAVEHY LRDQQLLGIW GCSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |