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Yorodumi- PDB-7lx2: Cryo-EM structure of ConSOSL.UFO.664 (ConS) in complex with bNAb ... -
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-Basic information
Entry | Database: PDB / ID: 7lx2 | ||||||
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Title | Cryo-EM structure of ConSOSL.UFO.664 (ConS) in complex with bNAb PGT122 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Env / SOSIP / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å | ||||||
Authors | Martin, G.M. / Ward, A.B. / Sattentau, Q.J. | ||||||
Funding support | 1items
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Citation | Journal: NPJ Vaccines / Year: 2023 Title: Profound structural conservation of chemically cross-linked HIV-1 envelope glycoprotein experimental vaccine antigens. Authors: Gregory M Martin / Rebecca A Russell / Philip Mundsperger / Scarlett Harris / Lu Jovanoska / Luiza Farache Trajano / Torben Schiffner / Katalin Fabian / Monica Tolazzi / Gabriella Scarlatti ...Authors: Gregory M Martin / Rebecca A Russell / Philip Mundsperger / Scarlett Harris / Lu Jovanoska / Luiza Farache Trajano / Torben Schiffner / Katalin Fabian / Monica Tolazzi / Gabriella Scarlatti / Leon McFarlane / Hannah Cheeseman / Yoann Aldon / Edith E Schermer / Marielle Breemen / Kwinten Sliepen / Dietmar Katinger / Renate Kunert / Rogier W Sanders / Robin Shattock / Andrew B Ward / Quentin J Sattentau / Abstract: Chemical cross-linking is used to stabilize protein structures with additional benefits of pathogen and toxin inactivation for vaccine use, but its use has been restricted by the potential for local ...Chemical cross-linking is used to stabilize protein structures with additional benefits of pathogen and toxin inactivation for vaccine use, but its use has been restricted by the potential for local or global structural distortion. This is of particular importance when the protein in question requires a high degree of structural conservation for inducing a biological outcome such as the elicitation of antibodies to conformationally sensitive epitopes. The HIV-1 envelope glycoprotein (Env) trimer is metastable and shifts between different conformational states, complicating its use as a vaccine antigen. Here we have used the hetero-bifunctional zero-length reagent 1-Ethyl-3-(3-Dimethylaminopropyl)-Carbodiimide (EDC) to cross-link two soluble Env trimers, selected well-folded trimer species using antibody affinity, and transferred this process to good manufacturing practice (GMP) for experimental medicine use. Cross-linking enhanced trimer stability to biophysical and enzyme attack. Cryo-EM analysis revealed that cross-linking retained the overall structure with root-mean-square deviations (RMSDs) between unmodified and cross-linked Env trimers of 0.4-0.5 Å. Despite this negligible distortion of global trimer structure, we identified individual inter-subunit, intra-subunit, and intra-protomer cross-links. Antigenicity and immunogenicity of the trimers were selectively modified by cross-linking, with cross-linked ConS retaining bnAb binding more consistently than ConM. Thus, the EDC cross-linking process improves trimer stability whilst maintaining protein folding, and is readily transferred to GMP, consistent with the more general use of this approach in protein-based vaccine design. | ||||||
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 | 7lx2.cif.gz | 520.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lx2.ent.gz | 423.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lx2_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 7lx2_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 7lx2_validation.xml.gz | 67.9 KB | Display | |
Data in CIF | 7lx2_validation.cif.gz | 103.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/7lx2 ftp://data.pdbj.org/pub/pdb/validation_reports/lx/7lx2 | HTTPS FTP |
-Related structure data
Related structure data | 23564MC 7lx3C 7lxmC 7lxnC 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 , 1 types, 3 molecules ABC
#1: Protein | Mass: 73136.742 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Cricetulus griseus (Chinese hamster) |
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-Antibody , 2 types, 6 molecules LMOHNP
#2: Antibody | Mass: 22880.275 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 25434.691 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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-Sugars , 5 types, 57 molecules
#4: 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 #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: 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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Molecular weight |
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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 | ||||||||||||||||||||||||
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161340 / Symmetry type: POINT |