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- EMDB-7896: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7896 | |||||||||
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Title | HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 | |||||||||
![]() | HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 | |||||||||
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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 / 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 / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.71 Å | |||||||||
![]() | Turner HL / Cottrell CA / Oyen D / Wilson IA / Ward AB | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization. Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner / ![]() ![]() Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
Images | ![]() | 22 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 424.8 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6didMC ![]() 7552C ![]() 7553C ![]() 7554C ![]() 7555C ![]() 7556C ![]() 7557C ![]() 7570C ![]() 7887C ![]() 7888C ![]() 7889C ![]() 7890C ![]() 7891C ![]() 7892C ![]() 7893C ![]() 7894C ![]() 7895C ![]() 7903C ![]() 7904C ![]() 7906C ![]() 6cjkC M: atomic model generated by this map C: citing same article ( |
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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 | HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3...
Entire | Name: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 |
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Components |
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-Supramolecule #1: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3...
Supramolecule | Name: HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Model includes fitted atomic structures for HIV Env BG505 SOSIP (PDB ID: 5v8m) and 10A Fab (PDB ID: 6cjk). |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 54.064277 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R |
-Macromolecule #2: Envelope glycoprotein gp160
Macromolecule | Name: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.146482 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD |
-Macromolecule #3: Monoclonal antibody 10A light chain
Macromolecule | Name: Monoclonal antibody 10A light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.047424 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVMTQTPAS VEAAVGGTVA IKCQASQSIR SYLAWYQQKP GQPPKLLIYE ASKLASGVPS RFSGSGSGTQ FTLTISGVEC DDAATYYCQ RNYDSYSGAY YPNGFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV CVANKYFPDV TVTWEVDGTT Q TTGIENSK ...String: DIVMTQTPAS VEAAVGGTVA IKCQASQSIR SYLAWYQQKP GQPPKLLIYE ASKLASGVPS RFSGSGSGTQ FTLTISGVEC DDAATYYCQ RNYDSYSGAY YPNGFGGGTE VVVKGDPVAP SVLIFPPAAD QVATGTVTIV CVANKYFPDV TVTWEVDGTT Q TTGIENSK TPQNSADCTY NLSSTLTLTS TQYNSHKEYT CKVTQGTTSV VQSFNRGDC |
-Macromolecule #4: Monoclonal antibody 10A heavy chain
Macromolecule | Name: Monoclonal antibody 10A heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.263018 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QLVESGGGLV QPGASLTLTC TASGFSFSSD YYMCWVRQAP GKGLEWIACI WTANSISYYA RWAKGRFTIS KTSSTTVTLQ MTSLTAADT ATYFCARGGS GDGQSLWGPG TLVTVSSGQP KAPSVFPLAP CCGDTPSSTV TLGCLVKGYL PEPVTVTWNS G TLTNGVRT ...String: QLVESGGGLV QPGASLTLTC TASGFSFSSD YYMCWVRQAP GKGLEWIACI WTANSISYYA RWAKGRFTIS KTSSTTVTLQ MTSLTAADT ATYFCARGGS GDGQSLWGPG TLVTVSSGQP KAPSVFPLAP CCGDTPSSTV TLGCLVKGYL PEPVTVTWNS G TLTNGVRT FPSVRQSSGL YSLSSVVSVT SSSQPVTCNV AHPATNTKVD KTVAPS |
-Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 21 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.6 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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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 - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average exposure time: 8.5 sec. / Average electron dose: 52.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-6did: |