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Yorodumi- PDB-6nf5: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nf5 | ||||||||||||
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Title | BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragmentantigen binding and base-binding RM20A3 fragment antigen binding | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/immune system / HIV-1 / HIV Envelope / SOSIP / antibody / trimer / precursor 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) Macaca mulatta (Rhesus monkey) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å | ||||||||||||
Authors | Ozorowski, G. / Torres, J.L. / 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 | 6nf5.cif.gz | 617.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nf5.ent.gz | 510.8 KB | Display | PDB format |
PDBx/mmJSON format | 6nf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nf5_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6nf5_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6nf5_validation.xml.gz | 97.6 KB | Display | |
Data in CIF | 6nf5_validation.cif.gz | 148.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/6nf5 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/6nf5 | HTTPS FTP |
-Related structure data
Related structure data | 7884MC 7875C 7876C 7885C 6dfgC 6dfhC 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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-Components
-HIV-1 Env BG505 MD64 N332-GT5 SOSIP ... , 2 types, 6 molecules ACJBDM
#1: Protein | Mass: 54236.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6*PLUS #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 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6*PLUS |
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-Antibody , 4 types, 12 molecules HEOLFPKGQNIR
#3: Antibody | Mass: 14151.747 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: 11253.285 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: V2-17 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #5: Antibody | Mass: 13511.111 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #6: Antibody | Mass: 13508.800 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) |
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-Sugars , 4 types, 54 molecules
#7: 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 #8: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: 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 | Name: BG505 MD64 N332-GT5 SOSIP trimer in complex with BG18-like precursor HMP1 fragment antigen binding and base-binding 8D11 fragment antigen binding Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.72 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Human immunodeficiency virus 1 | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Buffer solution | pH: 7.4 Details: Detergent (DDM) added immediately prior to grid preparation | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Complex was SEC purified | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2.5 nm / Nominal defocus min: 0.5 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 11.75 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1760 |
Image scans | Sampling size: 5 µm / Movie frames/image: 47 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94466 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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