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- PDB-8ymk: Localized reconstruction of Hepatitis B virus surface antigen dim... -

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Basic information

Entry
Database: PDB / ID: 8ymk
TitleLocalized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A0
ComponentsIsoform S of Large envelope protein
KeywordsVIRAL PROTEIN / Surface antigen / Localized reconstruction
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 / viral envelope / virion attachment to host cell / virion membrane / membrane / Large envelope protein
Function and homology information
Biological speciesHepatitis B virus ayw/China/Tibet127/2002
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, T. / Cao, L. / Mu, A. / Wang, Q. / Rao, Z.H.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)31971118 China
Ministry of Science and Technology (MoST, China)2017YFC0840300 China
Ministry of Science and Technology (MoST, China)2020YFA0707500 China
Chinese Academy of SciencesXDB08020200 China
Chinese Academy of SciencesXDB37020203 China
CitationJournal: Science / Year: 2024
Title: Inherent symmetry and flexibility in hepatitis B virus subviral particles.
Authors: Quan Wang / Tao Wang / Lin Cao / An Mu / Sheng Fu / Peipei Wang / Yan Gao / Wenxin Ji / Zhenyu Liu / Zhanqiang Du / Luke W Guddat / Wenchi Zhang / Shuang Li / Xuemei Li / Zhiyong Lou / ...Authors: Quan Wang / Tao Wang / Lin Cao / An Mu / Sheng Fu / Peipei Wang / Yan Gao / Wenxin Ji / Zhenyu Liu / Zhanqiang Du / Luke W Guddat / Wenchi Zhang / Shuang Li / Xuemei Li / Zhiyong Lou / Xiangxi Wang / Zhongyu Hu / Zihe Rao /
Abstract: Chronic hepatitis B virus (HBV) infection poses a major global health challenge with massive morbidity and mortality. Despite a preventive vaccine, current treatments provide limited virus clearance, ...Chronic hepatitis B virus (HBV) infection poses a major global health challenge with massive morbidity and mortality. Despite a preventive vaccine, current treatments provide limited virus clearance, necessitating lifelong commitment. The HBV surface antigen (HBsAg) is crucial for diagnosis and prognosis, yet its high-resolution structure and assembly on the virus envelope remain elusive. Utilizing extensive datasets and advanced cryo-electron microscopy analysis, we present structural insights into HBsAg at a near-atomic resolution of 3.7 angstroms. HBsAg homodimers assemble into subviral particles with - and -like quasisymmetry, elucidating the dense-packing rules and structural adaptability of HBsAg. These findings provide insights into how HBsAg assembles into higher-order filaments and interacts with the capsid to form virions.
History
DepositionMar 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: 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_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform S of Large envelope protein
B: Isoform S of Large envelope protein


Theoretical massNumber of molelcules
Total (without water)50,8162
Polymers50,8162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform S of Large envelope protein / L glycoprotein / L-HBsAg / LHB / Large S protein / Large surface protein / Major surface antigen


Mass: 25408.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus ayw/China/Tibet127/2002
Strain: isolate China/Tibet127/2002 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q913A6
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: Hepatitis B virus ayw/China/Tibet127/2002 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Hepatitis B virus ayw/China/Tibet127/2002
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 magnification: 22500 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 50 / Num. of real images: 157206
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10cryoSPARC2.15final Euler assignment
12cryoSPARC2.153D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10324877
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2864087 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8YMJ

8ymj


Pdb chain-ID: A / Accession code: 8YMJ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043008
ELECTRON MICROSCOPYf_angle_d0.8034168
ELECTRON MICROSCOPYf_dihedral_angle_d6.387462
ELECTRON MICROSCOPYf_chiral_restr0.046493
ELECTRON MICROSCOPYf_plane_restr0.006532

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