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- PDB-7ucg: Structure of the DU422 SOSIP.664 trimer in complex with neutraliz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ucg | ||||||||||||
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Title | Structure of the DU422 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24 | ||||||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / broadly neutralizing antibody / bNAb / HIV-1 / CD4 binding site / VH1-2 / VRC01-class / antiviral 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 / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...: / 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 / membrane => GO:0016020 / 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 / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Barnes, C.O. / Bjorkman, P.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C ...Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C Cetrulo Lorenzi / Alicja Piechocka-Trocha / Johannes F Scheid / Anthony P West / Bruce D Walker / Michael S Seaman / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman / ![]() ![]() Abstract: The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, ...The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 589.1 KB | Display | ![]() |
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PDB format | ![]() | 475.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26443MC ![]() 7uceC ![]() 7ucfC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Envelope glycoprotein ... , 2 types, 6 molecules BAMGIP
#1: Protein | Mass: 17104.527 Da / Num. of mol.: 3 / Fragment: UNP residues 509-659 / Mutation: Env mimic Source method: isolated from a genetically manipulated source Details: Env mimic DU422 SOSIP.664 / Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 56999.980 Da / Num. of mol.: 3 / Fragment: UNP residues 28-503 Source method: isolated from a genetically manipulated source Details: Env mimic DU422 SOSIP.664 / Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 3 molecules EFO
#3: Protein | Mass: 21925.209 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 3 types, 9 molecules DCNHJQLKR
#2: Antibody | Mass: 25498.590 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Antibody | Mass: 26389.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Antibody | Mass: 23708.293 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 48 molecules ![](data/chem/img/NAG.gif)
#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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-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 |
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Sample preparation
Component | Name: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES | ||||||||||||
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Molecular weight | Value: .65 MDa / Experimental value: YES | ||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1989 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 455671 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204220 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5CEZ | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.5 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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