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- EMDB-39396: Localized reconstruction of Hepatitis B virus surface antigen dim... -

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Basic information

Entry
Database: EMDB / ID: EMD-39396
TitleLocalized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A0
Map data
Sample
  • Virus: Hepatitis B virus ayw/China/Tibet127/2002
    • Protein or peptide: Isoform S of Large envelope protein
KeywordsSurface antigen / Localized reconstruction / VIRAL PROTEIN
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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang T / Cao L / Mu A / Wang Q / Rao ZH
Funding support China, 7 items
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, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39396.png

Downloads & links

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Map

FileDownload / File: emd_39396.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å		1.06 Å/pix.
x 288 pix.
= 305.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3054886 - 1.237415
Average (Standard dev.)-0.006636299 (±0.02910693)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39396_msk_1.map
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Additional map: Localized reconstruction from dataset A, generated by CryoSPARC...

Fileemd_39396_additional_1.map
AnnotationLocalized reconstruction from dataset A, generated by CryoSPARC local refinement job, and then resampled on the dataset A0 map (main map of this entry) in UCSF Chimera.
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39396_half_map_1.map
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Half map: #1

Fileemd_39396_half_map_2.map
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Sample components

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Entire : Hepatitis B virus ayw/China/Tibet127/2002

EntireName: Hepatitis B virus ayw/China/Tibet127/2002
Components
  • Virus: Hepatitis B virus ayw/China/Tibet127/2002
    • Protein or peptide: Isoform S of Large envelope protein

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Supramolecule #1: Hepatitis B virus ayw/China/Tibet127/2002

SupramoleculeName: Hepatitis B virus ayw/China/Tibet127/2002 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 489469 / Sci species name: Hepatitis B virus ayw/China/Tibet127/2002 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: Yes

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Macromolecule #1: Isoform S of Large envelope protein

MacromoleculeName: Isoform S of Large envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus ayw/China/Tibet127/2002 / Strain: isolate China/Tibet127/2002
Molecular weightTheoretical: 25.408059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPISNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCTTPAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA ...String:
MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPISNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCTTPAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA RFSWLSLLVP FVQWFVGLSP TVWLSVIWMM WYWGPSLYSI LSPFLPLLPI FFCLWVYI

UniProtKB: Large envelope protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 50 / Number real images: 157206 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10324877
Startup modelType of model: OTHER / Details: Reconstructed by subtracted sub-particles.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 2864087
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8ymj


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ymk:
Localized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A0

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