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- EMDB-43909: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463) | |||||||||
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![]() | HIV / Polyclonal / Antibodies / nsEMPEM / Rabbit / VIRAL PROTEIN | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
![]() | Brown S / Antansijevic A / 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. | |||||||||
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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) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
Images | ![]() | 455.1 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 33.1 MB 33.1 MB 33.1 MB 33.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 762.6 KB | Display | ![]() |
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Full document | ![]() | 762.1 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 13.6 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
-Additional map: Additional Map 1 - V2 and Base Epitopes
File | emd_43909_additional_1.map | ||||||||||||
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Annotation | Additional Map 1 - V2 and Base Epitopes | ||||||||||||
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Density Histograms |
-Additional map: Additional Map 2 - C3/V5 and V2 Epitopes
File | emd_43909_additional_2.map | ||||||||||||
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Annotation | Additional Map 2 - C3/V5 and V2 Epitopes | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_43909_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43909_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...
Entire | Name: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463) |
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Components |
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-Supramolecule #1: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...
Supramolecule | Name: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
Supramolecule | Name: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes type: complex / ID: 2 / Parent: 1 / Macromolecule list: all Details: Main Map - N611/N625 and V2 Epitopes Additional Map 1 - V2 and Base Epitopes Additional Map 2 - C3/V5 and V2 Epitopes |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: HIV-1 16055 SOSIP.v8.3 Env
Supramolecule | Name: HIV-1 16055 SOSIP.v8.3 Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HIV-1 16055 SOSIP.v8.3 - gp140
Macromolecule | Name: HIV-1 16055 SOSIP.v8.3 - gp140 / type: protein_or_peptide / ID: 1 / Details: The sequence contains engineered SOSIP mutations. / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
Sequence | String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK ...String: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK KQKVYALFYR LDIVPLEEER KGNSSKYRLI NCNTSAITQA CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEGEIIIRS ENLTNNVKTI IVHLNESVEI VCTRPNNNTV KSIRIGPGQW FYYTGDIIGN IRQAYCNIKK DDWIRTLQRV GKKLAEHFPR RIINFTQPAG GDLEITTHSF NCRGEFFYCN TSSLFNSTYN PNDTNSNSSS SNSSLDITIP CRIKQIINMW QRVGQAMYAP PIEGNITCKS NITGLLLVRD GGVESNETEI FRPGGGDMRN NWRSELYKYK VVEIKPLGIA PTRCKRRVVE RRRRRRAVGL GAVSFGFLGA AGSTMGAASI TLTVQARQLL SGIVQQQSNL LKAPECQQHL LQDGHWGIKQ LQTRVLAIEH YLKDQQLLGI WGCSGKLICC TAVPWNSSWS NKSHDEIWGN MTWMQWDREI SNYTNTIYRL LEDSQNQQEQ NEKDLLALD |
-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 / Pretreatment - Type: PLASMA CLEANING |
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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 |