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Yorodumi- PDB-7pc2: HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pc2 | ||||||
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Title | HIV-1 Env (BG505 SOSIP.664) in complex with the IgA bNAb 7-269 and the antibody 3BNC117. | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV / antibody / bNAb / Env | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Fernandez, I. / Bontems, F. / Pehau-Arnaudet, G. / Rey, F. | ||||||
Funding support | 1items
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Citation | Journal: J Exp Med / Year: 2022 Title: Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller. Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / ...Authors: Valérie Lorin / Ignacio Fernández / Guillemette Masse-Ranson / Mélanie Bouvin-Pley / Luis M Molinos-Albert / Cyril Planchais / Thierry Hieu / Gérard Péhau-Arnaudet / Dominik Hrebík / Giulia Girelli-Zubani / Oriane Fiquet / Florence Guivel-Benhassine / Rogier W Sanders / Bruce D Walker / Olivier Schwartz / Johannes F Scheid / Jordan D Dimitrov / Pavel Plevka / Martine Braibant / Michael S Seaman / François Bontems / James P Di Santo / Félix A Rey / Hugo Mouquet / Abstract: Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a ...Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers. | ||||||
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 | 7pc2.cif.gz | 607.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pc2.ent.gz | 521.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pc2_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 7pc2_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 7pc2_validation.xml.gz | 77.2 KB | Display | |
Data in CIF | 7pc2_validation.cif.gz | 111 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/7pc2 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/7pc2 | HTTPS FTP |
-Related structure data
Related structure data | 13316MC 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 ABCDEF
#3: Protein | Mass: 54064.277 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Strain: BG505 / Gene: env / Production host: Homo sapiens (human) #4: Protein | Mass: 17146.482 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus / Strain: BG505 / Gene: env / Production host: Homo sapiens (human) |
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-Antibody , 4 types, 12 molecules OMQPNRKGILHJ
#1: Antibody | Mass: 26425.404 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23520.053 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 24656.484 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #6: Antibody | Mass: 23022.658 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 9 types, 64 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 | 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 #11: Polysaccharide | Source method: isolated from a genetically manipulated source #12: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: Polysaccharide | Source method: isolated from a genetically manipulated source #14: Polysaccharide | Source method: isolated from a genetically manipulated source #15: 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: 8 | ||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 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: C-flat-2/2 | ||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 287 K |
-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 | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 |
-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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115394 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 5V8M |