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- EMDB-41275: CryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41275
TitleCryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in complex with Hepatitis C virus envelope glycoprotein E2
Map data
Sample
  • Complex: Ternary complex of CBH7-E2-HC84.26
    • Protein or peptide: CBH-7 Heavy chain
    • Protein or peptide: CBH-7 Light chain
    • Protein or peptide: envelope glycoprotein E2
    • Protein or peptide: HC84.26 Heavy chain
    • Protein or peptide: HC84.26 Light chain
KeywordsImmune system / vaccine target / E2 glycoprotein / HCV / ternary complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


host cell lipid droplet / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Hepacivirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsShahid S / Jiang L / Liu Y / Hasan SS / Mariuzza RA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI168048 United States
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM structures of HCV E2 glycoprotein bound to neutralizing and non-neutralizing antibodies determined using bivalent Fabs as fiducial markers.
Authors: Salman Shahid / Sharanbasappa S Karade / S Saif Hasan / Rui Yin / Liqun Jiang / Yanxin Liu / Nathaniel Felbinger / Liudmila Kulakova / Eric A Toth / Zhen-Yong Keck / Steven K H Foung / ...Authors: Salman Shahid / Sharanbasappa S Karade / S Saif Hasan / Rui Yin / Liqun Jiang / Yanxin Liu / Nathaniel Felbinger / Liudmila Kulakova / Eric A Toth / Zhen-Yong Keck / Steven K H Foung / Thomas R Fuerst / Brian G Pierce / Roy A Mariuzza /
Abstract: Global elimination of hepatitis C virus (HCV) will require an effective cross-genotype vaccine. The HCV E2 envelope glycoprotein is the main target of neutralizing antibodies but also contains ...Global elimination of hepatitis C virus (HCV) will require an effective cross-genotype vaccine. The HCV E2 envelope glycoprotein is the main target of neutralizing antibodies but also contains epitopes that elicit non-neutralizing antibodies which may provide protection through Fc effector functions rather than direct neutralization. We determined cryo-EM structures of a broadly neutralizing antibody, a moderately neutralizing antibody, and a non-neutralizing antibody bound to E2 to resolutions of 3.8, 3.3, and 3.7 Å, respectively. Whereas the broadly neutralizing antibody targeted the front layer of E2 and the non-neutralizing antibody targeted the back layer, the moderately neutralizing antibody straddled both front and back layers, and thereby defined a new neutralizing epitope on E2. The small size of complexes between conventional (monovalent) Fabs and E2 (~110 kDa) presented a challenge for cryo-EM. Accordingly, we engineered bivalent versions of E2-specific Fabs that doubled the size of Fab-E2 complexes and conferred highly identifiable shapes to the complexes that facilitated particle selection and orientation for image processing. This study validates bivalent Fabs as new fiducial markers for cryo-EM analysis of small proteins such as HCV E2 and identifies a new target epitope for vaccine development.
History
DepositionJul 18, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41275.png

Downloads & links

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Map

FileDownload / File: emd_41275.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2386196 - 2.0475736
Average (Standard dev.)-0.0003000488 (±0.029400777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41275_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_41275_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 : Ternary complex of CBH7-E2-HC84.26

EntireName: Ternary complex of CBH7-E2-HC84.26
Components
  • Complex: Ternary complex of CBH7-E2-HC84.26
    • Protein or peptide: CBH-7 Heavy chain
    • Protein or peptide: CBH-7 Light chain
    • Protein or peptide: envelope glycoprotein E2
    • Protein or peptide: HC84.26 Heavy chain
    • Protein or peptide: HC84.26 Light chain

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Supramolecule #1: Ternary complex of CBH7-E2-HC84.26

SupramoleculeName: Ternary complex of CBH7-E2-HC84.26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: CBH-7 Heavy chain

MacromoleculeName: CBH-7 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.417719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWRFLFV VAAATVQSQV QLVQSGAEVR KPGSSVKISC KASGGTFNNY ALSWVRQAPG QGLDWMGEIT PIFGTEKYAQ KFQGRVTIT ADESTNTLYM DLSSLRSEDS AVYYCARRGY IYGSPFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK ...String:
MDWTWRFLFV VAAATVQSQV QLVQSGAEVR KPGSSVKISC KASGGTFNNY ALSWVRQAPG QGLDWMGEIT PIFGTEKYAQ KFQGRVTIT ADESTNTLYM DLSSLRSEDS AVYYCARRGY IYGSPFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KS CDKTAGW SHPQFEK

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Macromolecule #2: CBH-7 Light chain

MacromoleculeName: CBH-7 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.477658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLRAR CDVLMTQSPS SLSASVGDRV TISCRASQSI SSFLNWYQQK PGKAPKLLIS AASSLSSGVP SRFSGSGSG TSFTLTISSL QPEDVATYYC QQSYSFLLTF GGGTNVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
MDMRVPAQLL GLLLLWLRAR CDVLMTQSPS SLSASVGDRV TISCRASQSI SSFLNWYQQK PGKAPKLLIS AASSLSSGVP SRFSGSGSG TSFTLTISSL QPEDVATYYC QQSYSFLLTF GGGTNVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: envelope glycoprotein E2

MacromoleculeName: envelope glycoprotein E2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepacivirus C
Molecular weightTheoretical: 32.28726 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DSTHVTGGTA SHTTRHFASL FSSGASQRVQ LINTNGSWHI NRTALNCNDS LHTGFLAALF YTHKFNASG CPERMAHCRP IDEFAQGWGP ITYAEGHGSD QRPYCWHYAP RQCGTIPASQ VCGPVYCFTP SPVVVGTTDR F GAPTYTWG ...String:
METDTLLLWV LLLWVPGSTG DSTHVTGGTA SHTTRHFASL FSSGASQRVQ LINTNGSWHI NRTALNCNDS LHTGFLAALF YTHKFNASG CPERMAHCRP IDEFAQGWGP ITYAEGHGSD QRPYCWHYAP RQCGTIPASQ VCGPVYCFTP SPVVVGTTDR F GAPTYTWG ENETDVLILN NTRPPQGNWF GCTWMNSTGF TKTCGGPPCN IGGVGNNTLT CPTDCFRKHP EATYTKCGSG PW LTPRCLV DYPYRLWHYP CTVNFTIFKV RMYVGGVEHR LNAACNIGHH HHHH

UniProtKB: Genome polyprotein

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Macromolecule #4: HC84.26 Heavy chain

MacromoleculeName: HC84.26 Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.356758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DQVQPVQSGA EVKKPGSSVK VSCEASGGTH SNYVITWVRQ APGQGLEWMG GFIPDFRTAM YAQGFQGRV TITADESTSL AYMELTNLRS EDTAVYYCAR GPLSRGYYDY WGPGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
METDTLLLWV LLLWVPGSTG DQVQPVQSGA EVKKPGSSVK VSCEASGGTH SNYVITWVRQ APGQGLEWMG GFIPDFRTAM YAQGFQGRV TITADESTSL AYMELTNLRS EDTAVYYCAR GPLSRGYYDY WGPGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCDKTA GWSHPQFEKT AATGACTCGA G

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Macromolecule #5: HC84.26 Light chain

MacromoleculeName: HC84.26 Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.35215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DSYVLTQPPS VSVAPGQTAS ITCSGDKLGD KYVSWYQQRP GQSPVLVLYQ DSKRPSGIPE RFSGSNSGN TATLTISGTQ AMDEADYYCQ AWDSSALVFG GGTKLTVLRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
METDTLLLWV LLLWVPGSTG DSYVLTQPPS VSVAPGQTAS ITCSGDKLGD KYVSWYQQRP GQSPVLVLYQ DSKRPSGIPE RFSGSNSGN TATLTISGTQ AMDEADYYCQ AWDSSALVFG GGTKLTVLRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl pH 8.0 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7058 / Average exposure time: 3.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270875
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6x9x

source_name: PDB, initial_model_type: experimental model

6mei

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-Correlation
Output model

PDB-8thz:
CryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in complex with Hepatitis C virus envelope glycoprotein E2

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