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- EMDB-27578: nsEM map of E1E2 AMS0232 glycoprotein in complex with monoclonal ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27578
TitlensEM map of E1E2 AMS0232 glycoprotein in complex with monoclonal antibody AR4A
Map datansEM map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A
Sample
  • Complex: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex with AR4A Fab
KeywordsHepatitis C virus / viral glycoprotein / antibody / complex / VIRAL PROTEIN
Biological speciesHepacivirus C
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsTorrents de la Pena A / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-008352 United States
CitationJournal: 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
DepositionJul 11, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27578.png

Downloads & links

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Map

FileDownload / File: emd_27578.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationnsEM map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-0.3757708 - 4.744189
Average (Standard dev.)-0.009025093 (±0.22434647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: nsEM half map of E1E2 AMS0232 glycoprotein complexed...

Fileemd_27578_half_map_1.map
AnnotationnsEM half map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: nsEM half map of E1E2 AMS0232 glycoprotein complexed...

Fileemd_27578_half_map_2.map
AnnotationnsEM half map of E1E2 AMS0232 glycoprotein complexed with monoclonal antibody AR4A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex wi...

EntireName: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex with AR4A Fab
Components
  • Complex: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex with AR4A Fab

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Supramolecule #1: nsEM map of E1E2 AMS0232 glycoprotein (Hepatitis C) in complex wi...

SupramoleculeName: 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
Source (natural)Organism: Hepacivirus C

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.018 mg/mL
BufferpH: 7.4 / Details: TBS
StainingType: NEGATIVE / Material: uranyl formate
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
DetailsE1E2 viral glycoprotein was complexed with AR4A Fab in a ratio of 1:3 (E1E2:Fab)

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 378
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3340
Initial angle assignmentType: OTHER / Details: Bayesian polishing
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Bayesian polishing
Final 3D classificationNumber classes: 3

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