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- PDB-9ugo: Cryo-EM structure of the HBsAg dimer and Complex with Fab -

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Basic information

Entry
Database: PDB / ID: 9ugo
TitleCryo-EM structure of the HBsAg dimer and Complex with Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Middle S protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HBV antigen / dimer / Fab / complex / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLiu, Y. / Liao, M. / Liu, Z. / Ju, B. / Zhang, Z.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab light chain
B: Fab heavy chain
C: Middle S protein
E: Middle S protein
D: Fab light chain
F: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)117,1116
Polymers117,1116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Fab light chain


Mass: 23425.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab heavy chain


Mass: 24121.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Middle S protein / HBsAg


Mass: 11008.200 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The sequence of organism hepatitis B virus genotype A is not available during the biocuration, replaced by B8QJB4 temporarily.
Source: (gene. exp.) hepatitis B virus genotype A
Production host: Yeast centromeric expression vector p416CYC (others)
References: UniProt: B8QJB4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of HBsAg dimer with Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21hepatitis B virus genotype A489455
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Yeast centromeric expression vector p416CYC (others)422498
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53213 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038283
ELECTRON MICROSCOPYf_angle_d0.61511272
ELECTRON MICROSCOPYf_dihedral_angle_d14.9241146
ELECTRON MICROSCOPYf_chiral_restr0.0441265
ELECTRON MICROSCOPYf_plane_restr0.0081440

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