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Yorodumi- PDB-6dfg: BG505 MD39 SOSIP trimer in complex with mature BG18 fragment anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dfg | ||||||||||||
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Title | BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / HIV Envelope / SOSIP / germline targeting / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | Function and homology information 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å | ||||||||||||
Authors | Ozorowski, G. / Steichen, J.M. / Schief, W.R. / Ward, A.B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2019 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dfg.cif.gz | 468.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dfg.ent.gz | 383.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dfg_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 6dfg_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6dfg_validation.xml.gz | 84.7 KB | Display | |
Data in CIF | 6dfg_validation.cif.gz | 124.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dfg ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dfg | HTTPS FTP |
-Related structure data
Related structure data | 7875MC 7876C 7884C 7885C 6dfhC 6nf5C 6nfcC 6oc7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 2 types, 6 molecules ACDBEF
#1: Protein | Mass: 53302.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 #2: Protein | Mass: 18250.541 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S8 |
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-Antibody , 2 types, 6 molecules HGILJK
#3: Antibody | Mass: 25043.186 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #4: Antibody | Mass: 22937.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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-Sugars , 7 types, 48 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: 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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Polysaccharide | Source method: isolated from a genetically manipulated source #11: 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 |
-Sample preparation
Component |
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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.: 4.75 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: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K / Details: 3.5 second blot time |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 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: 12 sec. / Electron dose: 62 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 691 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 48 |
-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: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45306 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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