+Open data
-Basic information
Entry | Database: PDB / ID: 6vo0 | ||||||||||||
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Title | BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / HIV / Env / antibody | ||||||||||||
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 | Oryctolagus cuniculus (rabbit) Human immunodeficiency virus 1 | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||
Authors | Nogal, B. / Cottrell, C.A. / Ward, A.B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2020 Title: HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite. Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin ...Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin / Hannah L Turner / Gabriel Ozorowski / Rogier W Sanders / Dennis R Burton / Andrew B Ward / Abstract: To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we ...To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we isolated monoclonal antibodies from a rabbit that did not exhibit glycan hole-dependent autologous serum neutralization. The antibodies did not compete with a previously isolated glycan hole-specific antibody but did compete with N332 glycan supersite broadly neutralizing antibodies. A 3.5-Å cryoEM structure of one of the antibodies in complex with the BG505 SOSIP.v5.2 trimer demonstrated that while the epitope recognized overlapped the N332 glycan supersite by contacting the GDIR motif at the base of V3, primary contacts were located in the variable V1 loop. These data suggest that strain-specific responses to V1 may interfere with broadly neutralizing responses to the N332 glycan supersite and vaccine immunogens may require engineering to minimize these off-target responses or steer them toward a more desirable pathway. | ||||||||||||
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 | 6vo0.cif.gz | 484.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vo0.ent.gz | 399.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vo0_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 6vo0_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6vo0_validation.xml.gz | 67.5 KB | Display | |
Data in CIF | 6vo0_validation.cif.gz | 103.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/6vo0 ftp://data.pdbj.org/pub/pdb/validation_reports/vo/6vo0 | HTTPS FTP |
-Related structure data
Related structure data | 21256MC 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
#3: Protein | Mass: 53268.371 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 #4: Protein | Mass: 17178.549 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 |
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-Antibody / Protein , 2 types, 6 molecules LJKHGI
#1: Antibody | Mass: 12078.307 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #2: Protein | Mass: 13025.553 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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-Sugars , 3 types, 48 molecules
#5: 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 #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: 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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85841 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |