+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5761 | |||||||||
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Title | Hepatitis C Virus E2 Envelope Glycoprotein Core Structure | |||||||||
Map data | E2 glycoprotein bound to AR2A Fab and CD81, single particle reconstruction | |||||||||
Sample |
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Keywords | hepatitis C / virus / envelope / glycoprotein | |||||||||
Biological species | Hepatitis C virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Nieusma T / Kong L / Giang E / Kadam RU / Cogburn KE / Hua Y / Dai X / Stanfield RL / Burton DR / Wilson IA ...Nieusma T / Kong L / Giang E / Kadam RU / Cogburn KE / Hua Y / Dai X / Stanfield RL / Burton DR / Wilson IA / Law M / Ward AB | |||||||||
Citation | Journal: Science / Year: 2013 Title: Hepatitis C virus E2 envelope glycoprotein core structure. Authors: Leopold Kong / Erick Giang / Travis Nieusma / Rameshwar U Kadam / Kristin E Cogburn / Yuanzi Hua / Xiaoping Dai / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson / Mansun Law / Abstract: Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host ...Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5761.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-5761-v30.xml emd-5761.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_5761_1.png | 63.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5761 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5761.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E2 glycoprotein bound to AR2A Fab and CD81, single particle reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : E2 glycoprotein bound to AR2A Fab and CD81
Entire | Name: E2 glycoprotein bound to AR2A Fab and CD81 |
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Components |
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-Supramolecule #1000: E2 glycoprotein bound to AR2A Fab and CD81
Supramolecule | Name: E2 glycoprotein bound to AR2A Fab and CD81 / type: sample / ID: 1000 / Number unique components: 3 |
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-Macromolecule #1: E2 envelope glycoprotein
Macromolecule | Name: E2 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: E2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Hepatitis C virus |
Molecular weight | Theoretical: 46 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: pCMV-Tag4A-tpa |
-Macromolecule #2: Antigen-binding fragment of antibody AR2A
Macromolecule | Name: Antigen-binding fragment of antibody AR2A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 50 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pComb3H |
-Macromolecule #3: CD81
Macromolecule | Name: CD81 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pComb3H |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: negative stain with uranyl formate |
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Grid | Details: 400 mesh copper |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55 |
Temperature | Average: 298 K |
Date | May 24, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 319 |
Tilt angle min | 0 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Appion, Spider, Xmipp, Eman1, Eman2 / Number images used: 32115 |
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Details | Particles were selected using automatic (difference-of-Gaussians) picking followed by reference-free classification to eliminate noisy picks or non-target aggregation states. |