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- EMDB-64142: Cryo-EM structure of the HBsAg dimer and Complex with Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-64142
TitleCryo-EM structure of the HBsAg dimer and Complex with Fab
Map data
Sample
  • Complex: complex of HBsAg dimer with Fab
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Middle S protein
KeywordsHBV antigen / dimer / Fab / complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / membrane fusion involved in viral entry into host cell / symbiont entry into host cell / virion attachment to host cell / virion membrane / Middle S protein
Function and homology information
Biological speciesHomo sapiens (human) / hepatitis B virus genotype A
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsLiu Y / Liao M / Liu Z / Ju B / Zhang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Gut / Year: 2026
Title: Characterisation of plasmablast-derived HBsAg-specific antibody and its structural basis for binding to native HBsAg dimer.
Authors: Bin Ju / Zhouqing Liu / Hu Yan / Yong Liu / Lu Zhang / Xiangyang Ge / Xin Wang / Zhu Si / Bing Zhou / Qing Fan / Miao Wang / Yuxiao Li / Wenlong Lai / Jianhui Gan / Haiyan Wang / Juanjuan ...Authors: Bin Ju / Zhouqing Liu / Hu Yan / Yong Liu / Lu Zhang / Xiangyang Ge / Xin Wang / Zhu Si / Bing Zhou / Qing Fan / Miao Wang / Yuxiao Li / Wenlong Lai / Jianhui Gan / Haiyan Wang / Juanjuan Zhao / Yuchen Xia / Maofu Liao / Zheng Zhang /
Abstract: BACKGROUND: Plasmablast-derived HBV surface antigen (HBsAg)-specific monoclonal antibody (mAb) and structural basis for binding to native HBsAg are poorly known.
OBJECTIVE: We aimed to identify plasmablast-derived HBsAg-specific mAbs, evaluate their antiviral activities and resolve their structure for binding to native HBsAg.
DESIGN: A previously vaccinated volunteer was enrolled in this study, who was boosted with a dose of recombinant hepatitis B vaccine and donated the blood sample. Activated plasmablasts were sorted ...DESIGN: A previously vaccinated volunteer was enrolled in this study, who was boosted with a dose of recombinant hepatitis B vaccine and donated the blood sample. Activated plasmablasts were sorted from fresh peripheral blood mononuclear cells and mAbs were expressed. Their gene features, cross-genotypic binding activities and antiviral functions in vitro and in vivo were comprehensively analysed. The cryo-electron microscopy (cryo-EM) was used to determine the structure of representative mAb bound to the native HBsAg.
RESULTS: In this study, we cloned a series of HBsAg-specific mAbs directly from clonally expanded plasmablasts from a vaccinated individual. Most of the mAbs displayed cross-reactivities of binding ...RESULTS: In this study, we cloned a series of HBsAg-specific mAbs directly from clonally expanded plasmablasts from a vaccinated individual. Most of the mAbs displayed cross-reactivities of binding to different genotype HBsAg proteins and antiviral functions such as neutralisation and antibody-dependent cellular phagocytosis. These human anti-HBsAg mAbs, especially SY-4-class and SY-23-class, could be good candidates for antibody drugs. The cryo-EM structure of SY-23 bound to the dimeric HBsAg was determined, revealing its binding mechanism and unprecedented structural detail of the major antigenic loop (AGL) of HBsAg.
CONCLUSION: Overall, our work has uncovered the diverse gene features and varied anti-HBV activities of plasmablast-derived mAbs, providing a series of antibody drug candidates and the long-sought- ...CONCLUSION: Overall, our work has uncovered the diverse gene features and varied anti-HBV activities of plasmablast-derived mAbs, providing a series of antibody drug candidates and the long-sought-after atomic model of AGL has paved the way for a wholistic characterisation of the AGL's dynamic conformation during HBV infection and immune response.
History
DepositionApr 13, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64142.png

Downloads & links

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Map

FileDownload / File: emd_64142.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.055961 - 0.09352878
Average (Standard dev.)0.00008498955 (±0.0025482667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64142_msk_1.map
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Additional map: #1

Fileemd_64142_additional_1.map
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Half map: #2

Fileemd_64142_half_map_1.map
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Half map: #1

Fileemd_64142_half_map_2.map
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Sample components

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Entire : complex of HBsAg dimer with Fab

EntireName: complex of HBsAg dimer with Fab
Components
  • Complex: complex of HBsAg dimer with Fab
    • Protein or peptide: Fab light chain
    • Protein or peptide: Fab heavy chain
    • Protein or peptide: Middle S protein

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Supramolecule #1: complex of HBsAg dimer with Fab

SupramoleculeName: complex of HBsAg dimer with Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.425979 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPAT LSVSPGERAT LSCRASQSVS NNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDSAVYYCQ QHHSWPPFTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSVSPGERAT LSCRASQSVS NNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDSAVYYCQ QHHSWPPFTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #2: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.12116 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV YCKASGGTFR SYGLNWVRQA PGQGLEWMGR IVPIFGISNF AQKFQGRFTI TADRSANTPY MELSSLRSE DTAVYYCVRG GAVAGAGSAG EGIFDYWDQG TLVIVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLVQSGAE VKKPGSSVKV YCKASGGTFR SYGLNWVRQA PGQGLEWMGR IVPIFGISNF AQKFQGRFTI TADRSANTPY MELSSLRSE DTAVYYCVRG GAVAGAGSAG EGIFDYWDQG TLVIVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS C

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Macromolecule #3: Middle S protein

MacromoleculeName: Middle S protein / type: protein_or_peptide / ID: 3
Details: The sequence of organism hepatitis B virus genotype A is not available during the biocuration, replaced by B8QJB4 temporarily.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: hepatitis B virus genotype A
Molecular weightTheoretical: 11.0082 KDa
Recombinant expressionOrganism: Yeast centromeric expression vector p416CYC (others)
SequenceString:
RWMCLRRFII FLFILLLCLI FLLVLLDYQG MLPVCPLIPG SSTTSTGPCR TCMTTAQGTS MYPSCCCTKP SDGNCTCIPI PSSWAFGKF LWEWASARF

UniProtKB: Middle S protein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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 AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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