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- PDB-9u9b: HBsAg in complex with HBC34 Fab -

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Basic information

Entry
Database: PDB / ID: 9u9b
TitleHBsAg in complex with HBC34 Fab
Components
  • HBC34 Fab Heavy Chain
  • HBC34 Fab Light Chain
  • Middle S protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HBV / HBsAg / Fab / Antigenic loop / VIRAL PROTEIN / 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 / membrane / Middle S protein
Function and homology information
Biological speciesHepatitis B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsChen, L. / He, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: Cell Discov / Year: 2025
Title: Structural polymorphism of the antigenic loop in HBV surface antigen dictates binding of diverse neutralizing antibodies.
Authors: Xiao He / Weiyu Tao / Yunlu Kang / Jiaxuan Xu / Xiaoyu Liu / Lei Chen /
Abstract: The Hepatitis B Virus (HBV) poses a significant health threat, causing millions of deaths each year. Hepatitis B surface antigen (HBsAg), the sole membrane protein on the HBV viral envelope, plays ...The Hepatitis B Virus (HBV) poses a significant health threat, causing millions of deaths each year. Hepatitis B surface antigen (HBsAg), the sole membrane protein on the HBV viral envelope, plays crucial roles in viral attachment to host cells and serves as the target for neutralizing antibodies (NAbs). Despite its functional and therapeutic significance, the mechanisms by which NAbs recognize HBsAg remain elusive. Here, we found that HBsAg proteins exist in distinct subtypes and are recognized by different groups of antibodies. Cryo-electron microscopy (Cryo-EM) structures of HBsAg dimers in complex with NAb Fab fragments reveal that the antigenic loop (AGL) of these distinct HBsAg types share a common structural core comprised of four β-strands. However, their surface structures exhibit unexpected polymorphism due to distinct disulfide bond linkages within the AGL region. This structural polymorphism determines the recognition of HBsAg by different groups of NAbs.
History
DepositionMar 27, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Middle S protein
B: Middle S protein
H: HBC34 Fab Heavy Chain
L: HBC34 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)108,8204
Polymers108,8204
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: Protein Middle S protein


Mass: 31153.318 Da / Num. of mol.: 2 / Mutation: C131A, C145A, C276A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: B5TFB1
#2: Antibody HBC34 Fab Heavy Chain


Mass: 23412.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody HBC34 Fab Light Chain


Mass: 23101.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
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: Structure of the Hepatitis B virus envelope protein in complex with HBC34 Fab
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Hepatitis B virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.41
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: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 206975 / Symmetry type: POINT

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