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- EMDB-70622: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70622
TitleHepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A and AR3C
Map dataHCV-1 sE1E2.Cut1 2.SPYdeltaN-His6bound to NAbs AR4A and AR3C
Sample
  • Complex: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A and AR3C
KeywordsHCV / E1E2 heterodimer / neutralizing antibody / vaccine antigen / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.97 Å
AuthorsJanus BM / Gonzalez FG / Ofek G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI168048 United States
CitationJournal: Nat Commun / Year: 2026
Title: Native-like soluble E1E2 glycoprotein heterodimers on self-assembling protein nanoparticles for hepatitis C virus vaccine design
Authors: Janus BM / Gonzalez FG / Ofek G
History
DepositionMay 14, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70622.png

Downloads & links

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Map

FileDownload / File: emd_70622.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHCV-1 sE1E2.Cut1 2.SPYdeltaN-His6bound to NAbs AR4A and AR3C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0501
Minimum - Maximum-0.2785037 - 0.5212062
Average (Standard dev.)-0.00026637048 (±0.015265215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70622_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70622_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A...

EntireName: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A and AR3C
Components
  • Complex: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A and AR3C

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Supramolecule #1: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A...

SupramoleculeName: Hepatitis C virus sE1E2.Cut1+2.SPYdeltaN bound to antibodies AR4A and AR3C
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.62 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174972
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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