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- PDB-9iyx: Structure of HBV surface antigen determined in recombinant spheri... -

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Basic information

Entry
Database: PDB / ID: 9iyx
TitleStructure of HBV surface antigen determined in recombinant spherical subviral particle
ComponentsLarge envelope protein
KeywordsVIRAL PROTEIN / HBV / HBsAg
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane / Large envelope protein
Function and homology information
Biological speciesHBV genotype D3 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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: Structure of small HBV surface antigen reveals mechanism of dimer formation.
Authors: Xiao He / Yunlu Kang / Weiyu Tao / Jiaxuan Xu / Xiaoyu Liu / Lei Chen /
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large envelope protein
B: Large envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9914
Polymers50,8602
Non-polymers1312
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 Large envelope protein / L glycoprotein / L-HBsAg / LHB / Large S protein / Large surface protein / Major surface antigen


Mass: 25430.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HBV genotype D3 (virus) / Production host: Homo sapiens (human) / References: UniProt: V9P415
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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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: HBV surface antigen dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: HBV genotype D3 (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: FEI TITAN 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1590360 / Symmetry type: POINT

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