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- PDB-8fsj: Cryo-EM structure of engineered hepatitis C virus E1E2 ectodomain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fsj | ||||||
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Title | Cryo-EM structure of engineered hepatitis C virus E1E2 ectodomain in complex with antibodies AR4A, HEPC74, and IGH520 | ||||||
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![]() | VIRAL PROTEIN / HCV / E1E2 | ||||||
Function / homology | ![]() host cell mitochondrial membrane / host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / virus-mediated perturbation of host defense response / viral envelope ...host cell mitochondrial membrane / host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / virus-mediated perturbation of host defense response / viral envelope / host cell nucleus / virion membrane / structural molecule activity / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å | ||||||
![]() | Metcalf, M.C. / Ofek, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies. Authors: Matthew C Metcalf / Benjamin M Janus / Rui Yin / Ruixue Wang / Johnathan D Guest / Edwin Pozharski / Mansun Law / Roy A Mariuzza / Eric A Toth / Brian G Pierce / Thomas R Fuerst / Gilad Ofek / ![]() Abstract: Hepatitis C virus (HCV) is a major global health burden as the leading causative agent of chronic liver disease and hepatocellular carcinoma. While the main antigenic target for HCV-neutralizing ...Hepatitis C virus (HCV) is a major global health burden as the leading causative agent of chronic liver disease and hepatocellular carcinoma. While the main antigenic target for HCV-neutralizing antibodies is the membrane-associated E1E2 surface glycoprotein, the development of effective vaccines has been hindered by complications in the biochemical preparation of soluble E1E2 ectodomains. Here, we present a cryo-EM structure of an engineered, secreted E1E2 ectodomain of genotype 1b in complex with neutralizing antibodies AR4A, HEPC74, and IGH520. Structural characterization of the E1 subunit and C-terminal regions of E2 reveal an overall architecture of E1E2 that concurs with that observed for non-engineered full-length E1E2. Analysis of the AR4A epitope within a region of E2 that bridges between the E2 core and E1 defines the structural basis for its broad neutralization. Our study presents the structure of an E1E2 complex liberated from membrane via a designed scaffold, one that maintains all essential structural features of native E1E2. The study advances the understanding of the E1E2 heterodimer structure, crucial for the rational design of secreted E1E2 antigens in vaccine development. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.3 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 47.8 KB | Display | |
Data in CIF | ![]() | 69.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29419MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 3 molecules EAC
#1: Protein | Mass: 42975.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1b09 / Plasmid: pCMV / Cell line (production host): HEK293 / Production host: ![]() |
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#4: Protein | Mass: 22951.379 Da / Num. of mol.: 1 / Fragment: residues 22-179 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1b09 / Plasmid: pCMV / Cell line (production host): HEK293 / Production host: ![]() |
#6: Protein | Mass: 31862.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody , 3 types, 3 molecules HLB
#2: Antibody | Mass: 27644.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23470.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Antibody | Mass: 25743.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 3 types, 14 molecules ![](data/chem/img/NAG.gif)
#7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: 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 #9: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: HCV E1E2 ectodomain in complex with AR4A, HEPC74, and IGH520 Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Molecular weight | Value: 0.250 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2620845 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143576 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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