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Yorodumi- PDB-7uoj: The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uoj | |||||||||
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Title | The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664 | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / envelope trimer / GP120 / GP41 / viral entry / type-1 membrane fusion glycoprotein / N49P9.6-FR3 / PGT121 / 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 / 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: 4.02 Å | |||||||||
Authors | Nguyen, D.N. / Tolbert, W.D. / Pazgier, M. | |||||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP Authors: Nguyen, D.N. / Tolbert, W.D. / Pazgier, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uoj.cif.gz | 602.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uoj.ent.gz | 484.9 KB | Display | PDB format |
PDBx/mmJSON format | 7uoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uoj_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 7uoj_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 7uoj_validation.xml.gz | 89.2 KB | Display | |
Data in CIF | 7uoj_validation.cif.gz | 136.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/7uoj ftp://data.pdbj.org/pub/pdb/validation_reports/uo/7uoj | HTTPS FTP |
-Related structure data
Related structure data | 26648MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Envelope glycoprotein ... , 2 types, 6 molecules GAIBCJ
#1: Protein | Mass: 54064.277 Da / Num. of mol.: 3 / Mutation: T330N,A498C Source method: isolated from a genetically manipulated source Details: Env mimic BG505 SOSIP.664 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK GnT1- 293 cells / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 #2: Protein | Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 / Mutation: I556P,T602C Source method: isolated from a genetically manipulated source Details: Env mimic BG505 SOSIP.664 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK Gnt1- 293 cells / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6 |
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-Antibody , 4 types, 12 molecules HDKLEMlemhdk
#3: Antibody | Mass: 25024.129 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) #4: Antibody | Mass: 21733.291 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) #5: Antibody | Mass: 22869.338 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) #6: Antibody | Mass: 25169.230 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human) |
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-Sugars , 6 types, 48 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: Polysaccharide | Source method: isolated from a genetically manipulated source #11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: 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 |
-Sample preparation
Component | Name: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs. Type: COMPLEX Details: Fab fragments were generated from papain digest of their respective IgGs. Each component was purified separately. Components were mixed and the complex was purified by gel filtration. Entity ID: #1-#6 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.2 / Details: Phosphate buffered saline | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Quantifoil R1.2/1.3 | ||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 2700 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4368 |
-Processing
EM software |
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Image processing | Details: Data sets from two grid types were combined into a single data set. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3151423 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132055 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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