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Yorodumi- EMDB-27578: nsEM map of E1E2 AMS0232 glycoprotein in complex with monoclonal ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27578 | |||||||||
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Title | nsEM map of E1E2 AMS0232 glycoprotein in complex with monoclonal antibody AR4A | |||||||||
Map data | nsEM map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A | |||||||||
Sample |
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Keywords | Hepatitis C virus / viral glycoprotein / antibody / complex / VIRAL PROTEIN | |||||||||
Biological species | Hepacivirus C | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Torrents de la Pena A / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2022 Title: Structure of the hepatitis C virus E1E2 glycoprotein complex. Authors: Alba Torrents de la Peña / Kwinten Sliepen / Lisa Eshun-Wilson / Maddy L Newby / Joel D Allen / Ian Zon / Sylvie Koekkoek / Ana Chumbe / Max Crispin / Janke Schinkel / Gabriel C Lander / ...Authors: Alba Torrents de la Peña / Kwinten Sliepen / Lisa Eshun-Wilson / Maddy L Newby / Joel D Allen / Ian Zon / Sylvie Koekkoek / Ana Chumbe / Max Crispin / Janke Schinkel / Gabriel C Lander / Rogier W Sanders / Andrew B Ward / Abstract: Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope ...Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope E1 and E2 glycoproteins are essential for viral entry and comprise the primary antigenic target for neutralizing antibody responses. The molecular mechanisms of E1E2 assembly, as well as how the E1E2 heterodimer binds broadly neutralizing antibodies, remain elusive. Here, we present the cryo-electron microscopy structure of the membrane-extracted full-length E1E2 heterodimer in complex with three broadly neutralizing antibodies-AR4A, AT1209, and IGH505-at ~3.5-angstrom resolution. We resolve the interface between the E1 and E2 ectodomains and deliver a blueprint for the rational design of vaccine immunogens and antiviral drugs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27578.map.gz | 30.8 MB | EMDB map data format | |
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Header (meta data) | emd-27578-v30.xml emd-27578.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
Images | emd_27578.png | 14.7 KB | ||
Filedesc metadata | emd-27578.cif.gz | 4.2 KB | ||
Others | emd_27578_half_map_1.map.gz emd_27578_half_map_2.map.gz | 59.5 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27578 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27578 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27578.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | nsEM map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: nsEM half map of E1E2 AMS0232 glycoprotein complexed...
File | emd_27578_half_map_1.map | ||||||||||||
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Annotation | nsEM half map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: nsEM half map of E1E2 AMS0232 glycoprotein complexed...
File | emd_27578_half_map_2.map | ||||||||||||
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Annotation | nsEM half map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex wi...
Entire | Name: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex with AR4A Fab |
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Components |
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-Supramolecule #1: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex wi...
Supramolecule | Name: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex with AR4A Fab type: complex / ID: 1 / Parent: 0 Details: Fab fragment generated by cleavage of IgG antibody by papain |
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Source (natural) | Organism: Hepacivirus C |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.018 mg/mL |
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Buffer | pH: 7.4 / Details: TBS |
Staining | Type: NEGATIVE / Material: uranyl formate |
Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Details | E1E2 viral glycoprotein was complexed with AR4A Fab in a ratio of 1:3 (E1E2:Fab) |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 378 |
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Startup model | Type of model: NONE |
Initial angle assignment | Type: OTHER / Details: Bayesian polishing |
Final 3D classification | Number classes: 3 |
Final angle assignment | Type: OTHER / Software - Name: RELION (ver. 3.0) / Details: Bayesian polishing |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3340 |