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Open data
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Basic information
| Entry | Database: PDB / ID: 6udj | |||||||||
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| Title | HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074 | |||||||||
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 broadly neutralizing antibody / Env / cryo-EM / bNAb / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
| Function / homology | Function and homology informationimmunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human)![]() Human immunodeficiency virus 1 | |||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Abernathy, M.E. / Barnes, C.O. / Gristick, H.B. / Bjorkman, P.J. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2020Title: Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Authors: Philipp Schommers / Henning Gruell / Morgan E Abernathy / My-Kim Tran / Adam S Dingens / Harry B Gristick / Christopher O Barnes / Till Schoofs / Maike Schlotz / Kanika Vanshylla / Christoph ...Authors: Philipp Schommers / Henning Gruell / Morgan E Abernathy / My-Kim Tran / Adam S Dingens / Harry B Gristick / Christopher O Barnes / Till Schoofs / Maike Schlotz / Kanika Vanshylla / Christoph Kreer / Daniela Weiland / Udo Holtick / Christof Scheid / Markus M Valter / Marit J van Gils / Rogier W Sanders / Jörg J Vehreschild / Oliver A Cornely / Clara Lehmann / Gerd Fätkenheuer / Michael S Seaman / Jesse D Bloom / Pamela J Bjorkman / Florian Klein / ![]() Abstract: Broadly neutralizing antibodies (bNAbs) represent a promising approach to prevent and treat HIV-1 infection. However, viral escape through mutation of the HIV-1 envelope glycoprotein (Env) limits ...Broadly neutralizing antibodies (bNAbs) represent a promising approach to prevent and treat HIV-1 infection. However, viral escape through mutation of the HIV-1 envelope glycoprotein (Env) limits clinical applications. Here we describe 1-18, a new V1-46-encoded CD4 binding site (CD4bs) bNAb with outstanding breadth (97%) and potency (GeoMean IC = 0.048 μg/mL). Notably, 1-18 is not susceptible to typical CD4bs escape mutations and effectively overcomes HIV-1 resistance to other CD4bs bNAbs. Moreover, mutational antigenic profiling uncovered restricted pathways of HIV-1 escape. Of most promise for therapeutic use, even 1-18 alone fully suppressed viremia in HIV-1-infected humanized mice without selecting for resistant viral variants. A 2.5-Å cryo-EM structure of a 1-18-BG505 Env complex revealed that these characteristics are likely facilitated by a heavy-chain insertion and increased inter-protomer contacts. The ability of 1-18 to effectively restrict HIV-1 escape pathways provides a new option to successfully prevent and treat HIV-1 infection. | |||||||||
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Structure visualization
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6udj.cif.gz | 621.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6udj.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 6udj.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6udj_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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| Full document | 6udj_full_validation.pdf.gz | 4.4 MB | Display | |
| Data in XML | 6udj_validation.xml.gz | 92.1 KB | Display | |
| Data in CIF | 6udj_validation.cif.gz | 145.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6udj ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6udj | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 20739MC ![]() 6udkC M: map data used to model this data C: citing same article ( |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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Components
-Envelope glycoprotein ... , 2 types, 6 molecules CMFGJP
| #5: Protein | Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Human immunodeficiency virus 1 / Gene: env / Cell (production host): CHO / Production host: ![]() #6: Protein | Mass: 53864.086 Da / Num. of mol.: 3 / Fragment: UNP residues 32-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Human immunodeficiency virus 1 / Gene: env / Cell (production host): CHO / Production host: ![]() |
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-Antibody , 4 types, 12 molecules AKQEOIBLRDNH
| #1: Antibody | Mass: 25661.688 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Production host: Homo sapiens (human) / References: UniProt: S6B2B6#2: Antibody | Mass: 25330.389 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8#3: Antibody | Mass: 23180.760 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Production host: Homo sapiens (human) / References: UniProt: Q8N355#4: Antibody | Mass: 53133.797 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi 293 / Production host: Homo sapiens (human) |
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-Sugars , 7 types, 60 molecules 
| #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: 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 #9: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #10: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #13: Sugar | ChemComp-NAG / |
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-Non-polymers , 1 types, 45 molecules 
| #14: Water | ChemComp-HOH / |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-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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| Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
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| Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
| Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: 0 blot force, 3.0 second blot time, 3 uL sample added to freshly glow discharged grids |
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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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1256 |
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Processing
| Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | |||||||||||||||||||||||||||||||||||
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 230924 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||
| Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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About Yorodumi




Homo sapiens (human)
Human immunodeficiency virus 1
United States, 2items
Citation

UCSF Chimera







PDBj










