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- PDB-9ubq: HBsAg in complex with H020 Fab -

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Basic information

Entry
Database: PDB / ID: 9ubq
TitleHBsAg in complex with H020 Fab
Components
  • H020 Fab Heavy Chain
  • H020 Fab Light Chain
  • Middle S protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HBV / HBsAg / Fab / Antigentic 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: 2.86 Å
AuthorsChen, L. / Tao, W. / He, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: J Mol Biol / Year: 2025
Title: The Symmetric Structure of the Antigenic Loop in Type B HBV Surface Antigen.
Authors: Weiyu Tao / Xiao He / Lei Chen /
Abstract: Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral ...Hepatitis B virus (HBV) is an enveloped virus with HBV surface antigen (HBsAg) as the only protein on its viral membrane. The extracellular antigenic loop (AGL) of HBsAg plays a crucial role in viral attachment to host cells, serves as the primary target for neutralizing antibodies (NAbs), and is subject to escape mutations. Previous studies have shown that the AGL exhibits two different structures (Type A and Type B) dictated by distinct disulfide bond linkage. However, due to the flexibility of some regions in previous structure, the complete model of AGL and its symmetry remain elusive. Here, we present the cryo-EM structure of AGL in complex with the Fab fragment of the NAb H020. The complete structure of AGL reveals its two-fold symmetry and it can bind two Fab fragments simultaneously. Further analysis elucidates the underlying mechanism of pan-serotype neutralizing capability of H020 and how escape mutations hinder its binding.
History
DepositionApr 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 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
C: H020 Fab Heavy Chain
D: H020 Fab Light Chain
B: Middle S protein
E: H020 Fab Heavy Chain
F: H020 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)155,9896
Polymers155,9896
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 H020 Fab Heavy Chain


Mass: 23662.443 Da / Num. of mol.: 2
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 H020 Fab Light Chain


Mass: 23178.699 Da / Num. of mol.: 2
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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of the Hepatitis B virus envelope protein in complex with H020 FabCOMPLEXall0RECOMBINANT
2envelope proteinCOMPLEX#11RECOMBINANT
3H020 FabCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Hepatitis B virus10407
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 52 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195817 / Symmetry type: POINT

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