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- PDB-8t2e: BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8t2e | ||||||||||||
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Title | BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP3 | ||||||||||||
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![]() | VIRAL PROTEIN / HIV-1 / Env / NHP / Antibody / Fusion Peptide / Polyclonal | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Pratap, P.P. / Antansijevic, A. / Ozorowski, G. / Ward, A.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Priming antibody responses to the fusion peptide in rhesus macaques. Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Joel D ...Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Joel D Allen / Bartek Nogal / Murillo Silva / Jinal Bhiman / Matthias Pauthner / Darrell J Irvine / David Montefiori / Max Crispin / Dennis R Burton / Guido Silvestri / Shane Crotty / Andrew B Ward / ![]() ![]() Abstract: Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies ...Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to prime and elicit antibody responses against the conserved fusion peptide (FP). GC responses and antibody specificities were tracked longitudinally using lymph node fine-needle aspirates and electron microscopy polyclonal epitope mapping (EMPEM), respectively, to show antibody responses to the FP/N611 glycan hole region were primed, although exhibited limited neutralization breadth. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 377.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 40981MC ![]() 8swvC ![]() 8swwC ![]() 8swxC ![]() 8t2fC C: citing same article ( M: map data used to model this data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 4 types, 8 molecules AEFBCDHL
#1: Protein | Mass: 58090.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 17192.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 8528.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 3 types, 56 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | #7: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 0.470 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 41.3591843915 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7339 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88235 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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