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- EMDB-73824: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with A... -

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Basic information

Entry
Database: EMDB / ID: EMD-73824
TitleCryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab
Map dataSharpened map
Sample
  • Complex: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab
    • Protein or peptide: sE1E2
    • Protein or peptide: AT1211 Heavy Chain
    • Protein or peptide: AT1211 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHepatitis C / broadly neutralizing antibody / soluble antigen / VIRAL PROTEIN
Biological speciesHepacivirus hominis / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsCannac F / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure-based design of stable recombinant hepatitis C virus E1E2 heterodimers
Authors: Capella-Pujol J / Mulder F
History
DepositionNov 12, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73824.png

Downloads & links

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Map

FileDownload / File: emd_73824.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 300 pix.
= 215.4 Å		0.72 Å/pix.
x 300 pix.
= 215.4 Å		0.72 Å/pix.
x 300 pix.
= 215.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.9174055 - 1.2462103
Average (Standard dev.)0.000060473427 (±0.020826073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 215.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73824_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_73824_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_73824_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of a soluble HCV E1E2 antigen in complex with A...

EntireName: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab
Components
  • Complex: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab
    • Protein or peptide: sE1E2
    • Protein or peptide: AT1211 Heavy Chain
    • Protein or peptide: AT1211 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with A...

SupramoleculeName: Cryo-EM structure of a soluble HCV E1E2 antigen in complex with AT1211 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Hepacivirus hominis

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Macromolecule #1: sE1E2

MacromoleculeName: sE1E2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepacivirus hominis
Molecular weightTheoretical: 64.587008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YQVRNSTGLY HVTNDCPNSS IVYETADAIL HTPGCVPCVR EGNASRCWVP MTCTVATRDG KLPATQLRRG GSGGSGGSPR RHWTTQDCN CSIYPGHVTG HRMAWDMMMN PSPTTALVVA QLLRIPQAIL DMIAPGGRIA RLEEKVKTLK AQNSELASTA N MLREQVAQ ...String:
YQVRNSTGLY HVTNDCPNSS IVYETADAIL HTPGCVPCVR EGNASRCWVP MTCTVATRDG KLPATQLRRG GSGGSGGSPR RHWTTQDCN CSIYPGHVTG HRMAWDMMMN PSPTTALVVA QLLRIPQAIL DMIAPGGRIA RLEEKVKTLK AQNSELASTA N MLREQVAQ LKQKVMNYRR RRRRQTYVTG GTAARATSGL ANFFSPGAKQ DVQLINTNGS WHINRTALNC NTSLETGWIA GL IYLNKFN SSGCPERMAS CRPLADFAQG WGPISYANGS GPDHRPYCWH YPPKPCGIVS AKSVCGPVYC FTPSPVVVGT TNK LGAPTY SWGENETDVF VLNNTRPPLG NWFGCTWMNS TGFTKVCGAP PCAIGGVGNN TLHCPTDCFR KHPEATYSRC GSGP WITPR CLVDYPYRLW HYPCTANYTR FKVRMYIGGV EHRLDAACNW TRGERCDLED RDRSELSPLL LSTTQWQVLP CSFTT PPAL SCGLIHLHQN IVDVQYLYGV GSSIVSWAIP GGLTDTLQAE TDQLEDKKSA LQTEIANLLK EKEKLEFILA AYGGSA WSH PQFEKGGGSG GGSGGSSAWS HPQFEK

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Macromolecule #2: AT1211 Heavy Chain

MacromoleculeName: AT1211 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.437383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFS GYGITWVRQA PGQGLEWMGT IIPVSATETY AQRLQGRVTI SADEHSTTSY MEVSSLKSE DTALYYCARH DYFWGTPLDI WGQGTMVIVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFS GYGITWVRQA PGQGLEWMGT IIPVSATETY AQRLQGRVTI SADEHSTTSY MEVSSLKSE DTALYYCARH DYFWGTPLDI WGQGTMVIVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCHHHHH H

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Macromolecule #3: AT1211 Light Chain

MacromoleculeName: AT1211 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.480043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPDF QSVTPKEKVT ITCRASQSIG SNLHWYQQKP GQSPKLLIKY ASQSFSGVPS RFSGSGSGTD FTLTINSLEA EDAATYFCH QSYNLPRTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPDF QSVTPKEKVT ITCRASQSIG SNLHWYQQKP GQSPKLLIKY ASQSFSGVPS RFSGSGSGTD FTLTINSLEA EDAATYFCH QSYNLPRTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTRS FNRGEC

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 1827 / Average exposure time: 6.2 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 164770
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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