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Yorodumi- PDB-6vlr: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PG... -
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-Basic information
Entry | Database: PDB / ID: 6vlr | ||||||||||||||||||
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Title | BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 and PGT122 Fab | ||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HIV / antibody / Fab / vaccine / 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: 4.42 Å | ||||||||||||||||||
Authors | Cottrell, C.A. / Ward, A.B. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: PLoS Pathog / Year: 2020 Title: Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates. Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / ...Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils / Abstract: The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies. #1: Journal: Biorxiv / Year: 2020 Title: Mapping the immunogenic landscape of native HIV-1 envelope trimers in non-human primates Authors: Cottrell, C.A. / van Schooten, J. / Bowman, C.A. / Yuan, M. / Oyen, D. / Shin, M. / Morpurgo, R. / van der Woude, P. / van Breemen, M. / Torres, J.L. / Patel, R. / Gross, J. / Sewall, L.M. / ...Authors: Cottrell, C.A. / van Schooten, J. / Bowman, C.A. / Yuan, M. / Oyen, D. / Shin, M. / Morpurgo, R. / van der Woude, P. / van Breemen, M. / Torres, J.L. / Patel, R. / Gross, J. / Sewall, L.M. / Copps, J. / Ozorowski, G. / Sok, D. / Rakasz, E.G. / Labranche, C. / Vigdorovich, V. / Christley, S. / Sather, D.N. / Montefiori, D. / Moore, J.P. / Burton, D.R. / Wilson, I.A. / Sanders, R.W. / Ward, A.B. / van Gils, M.J. | ||||||||||||||||||
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 | 6vlr.cif.gz | 552.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vlr.ent.gz | 451.4 KB | Display | PDB format |
PDBx/mmJSON format | 6vlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vlr_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6vlr_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 6vlr_validation.xml.gz | 86.4 KB | Display | |
Data in CIF | 6vlr_validation.cif.gz | 130 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vlr ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vlr | HTTPS FTP |
-Related structure data
Related structure data | 21232MC 6vn0C 6vo1C 6vorC 6vosC 6vsrC 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
-Protein , 2 types, 6 molecules AHGBJI
#1: 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 #2: 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 , 4 types, 8 molecules CDELKMFN
#3: Antibody | Mass: 14838.731 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 11510.612 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) #5: Antibody | | Mass: 13878.558 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human) #6: Antibody | | Mass: 12370.759 Da / Num. of mol.: 1 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) |
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-Sugars , 6 types, 43 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 | 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 #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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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 |
-Sample preparation
Component | Name: BG505 SOSIP.v5.2 in complex with rhesus macaque Fab RM20E1 Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES | ||||||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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 / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 51.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 48 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17010 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL |