+Open data
-Basic information
Entry | Database: PDB / ID: 8f7t | ||||||
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Title | Glycan-Base ConC Env Trimer | ||||||
Components |
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Keywords | VIRAL PROTEIN / HIV-1 / Glycan / Env | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Olia, A.S. / Kwong, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: iScience / Year: 2023 Title: Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases. Authors: Adam S Olia / Cheng Cheng / Tongqing Zhou / Andrea Biju / Darcy R Harris / Anita Changela / Hongying Duan / Vera B Ivleva / Wing-Pui Kong / Li Ou / Reda Rawi / Yaroslav Tsybovsky / David J ...Authors: Adam S Olia / Cheng Cheng / Tongqing Zhou / Andrea Biju / Darcy R Harris / Anita Changela / Hongying Duan / Vera B Ivleva / Wing-Pui Kong / Li Ou / Reda Rawi / Yaroslav Tsybovsky / David J Van Wazer / Angela R Corrigan / Christopher A Gonelli / Myungjin Lee / Krisha McKee / Sandeep Narpala / Sijy O'Dell / Danealle K Parchment / Erik-Stephane D Stancofski / Tyler Stephens / Ivy Tan / I-Ting Teng / Shuishu Wang / Qing Wei / Yongping Yang / Zhengrong Yang / Baoshan Zhang / / Jan Novak / Matthew B Renfrow / Nicole A Doria-Rose / Richard A Koup / Adrian B McDermott / Jason G Gall / Q Paula Lei / John R Mascola / Peter D Kwong / Abstract: Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess ...Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential -linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f7t.cif.gz | 301 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f7t.ent.gz | 242.9 KB | Display | PDB format |
PDBx/mmJSON format | 8f7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f7t_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8f7t_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8f7t_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 8f7t_validation.cif.gz | 89 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/8f7t ftp://data.pdbj.org/pub/pdb/validation_reports/f7/8f7t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 17547.807 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293Freestyle / Production host: Homo sapiens (human) #2: Protein | Mass: 54495.898 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): 293Freestyle / Production host: Homo sapiens (human) #3: Polysaccharide | #4: Sugar | ChemComp-NAG / 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: HIV-1 Consensus C Env trimer with glycan covered base / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: 293Freestyle |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 297 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 / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 43.54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12967 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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