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- PDB-6dfh: BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dfh | ||||||||||||
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Title | BG505 MD64 N332-GT2 SOSIP trimer in complex with germline-reverted BG18 fragment antigen binding | ||||||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / HIV Envelope / SOSIP / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å | ||||||||||||
![]() | Ozorowski, G. / Steichen, J.M. / Schief, W.R. / Ward, A.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses. Authors: Jon M Steichen / Ying-Cing Lin / Colin Havenar-Daughton / Simone Pecetta / Gabriel Ozorowski / Jordan R Willis / Laura Toy / Devin Sok / Alessia Liguori / Sven Kratochvil / Jonathan L Torres ...Authors: Jon M Steichen / Ying-Cing Lin / Colin Havenar-Daughton / Simone Pecetta / Gabriel Ozorowski / Jordan R Willis / Laura Toy / Devin Sok / Alessia Liguori / Sven Kratochvil / Jonathan L Torres / Oleksandr Kalyuzhniy / Eleonora Melzi / Daniel W Kulp / Sebastian Raemisch / Xiaozhen Hu / Steffen M Bernard / Erik Georgeson / Nicole Phelps / Yumiko Adachi / Michael Kubitz / Elise Landais / Jeffrey Umotoy / Amanda Robinson / Bryan Briney / Ian A Wilson / Dennis R Burton / Andrew B Ward / Shane Crotty / Facundo D Batista / William R Schief / ![]() Abstract: Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for ...Vaccine induction of broadly neutralizing antibodies (bnAbs) to HIV remains a major challenge. Germline-targeting immunogens hold promise for initiating the induction of certain bnAb classes; yet for most bnAbs, a strong dependence on antibody heavy chain complementarity-determining region 3 (HCDR3) is a major barrier. Exploiting ultradeep human antibody sequencing data, we identified a diverse set of potential antibody precursors for a bnAb with dominant HCDR3 contacts. We then developed HIV envelope trimer-based immunogens that primed responses from rare bnAb-precursor B cells in a mouse model and bound a range of potential bnAb-precursor human naïve B cells in ex vivo screens. Our repertoire-guided germline-targeting approach provides a framework for priming the induction of many HIV bnAbs and could be applied to most HCDR3-dominant antibodies from other pathogens. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 462.9 KB | Display | ![]() |
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PDB format | ![]() | 376.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 80.4 KB | Display | |
Data in CIF | ![]() | 120.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7876MC ![]() 7875C ![]() 7884C ![]() 7885C ![]() 6dfgC ![]() 6nf5C ![]() 6nfcC ![]() 6oc7C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Envelope glycoprotein ... , 2 types, 6 molecules ACDBEF
#1: Protein | Mass: 53497.836 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 18209.594 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Antibody , 2 types, 6 molecules HGILJK
#3: Antibody | Mass: 24602.631 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 22861.195 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 42 molecules ![](data/chem/img/NAG.gif)
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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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: 0.57 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Natural host | Organism: Homo sapiens | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: Gatan Model 950 Advanced Plasma System / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2 4C | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: 5 second blot time |
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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: 29000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 65 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1031 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 40 |
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Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46273 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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