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- EMDB-39404: Localized reconstruction of Hepatitis B virus surface antigen dim... -

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Basic information

Entry
Database: EMDB / ID: EMD-39404
TitleLocalized reconstruction of Hepatitis B virus surface antigen dimer in the subviral particle with D2 symmetry from dataset A
Map dataThe main map refined by CryoSPARC and sharpened by RELION using auto-tightening FSC mask.
Sample
  • Virus: Hepatitis B virus ayw/China/Tibet127/2002
    • Protein or peptide: Small Hepatitis B virus surface antigen
KeywordsSurface antigen / Localized reconstruction / VIRAL PROTEIN
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-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39404.png

Downloads & links

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Map

FileDownload / File: emd_39404.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map refined by CryoSPARC and sharpened by RELION using auto-tightening FSC mask.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å		1.06 Å/pix.
x 180 pix.
= 190.8 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.34853724 - 0.2409596
Average (Standard dev.)0.00013847457 (±0.007628992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39404_msk_1.map
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Additional map: The same as main map but resampled on...

Fileemd_39404_additional_1.map
AnnotationThe same as main map but resampled on the localized reconstruction from dataset A0 in UCSF Chimera.
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Additional map: One of half maps generated by the original...

Fileemd_39404_additional_2.map
AnnotationOne of half maps generated by the original CryoSPARC local refinement job.
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Additional map: The sharpened map generated by DeepEMhancer using the...

Fileemd_39404_additional_3.map
AnnotationThe sharpened map generated by DeepEMhancer using the original CryoSPARC local refinement maps as input.
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Additional map: One of half maps generated by the original...

Fileemd_39404_additional_4.map
AnnotationOne of half maps generated by the original CryoSPARC local refinement job.
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AxesZYX

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Additional map: The sharpened map from the original CryoSPARC local refinement job.

Fileemd_39404_additional_5.map
AnnotationThe sharpened map from the original CryoSPARC local refinement job.
Projections & Slices
AxesZYX

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Histogram

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Half map: One of half maps reconstructed by RELION 'relion reconstruct'...

Fileemd_39404_half_map_1.map
AnnotationOne of half maps reconstructed by RELION 'relion_reconstruct' command using alignment parameters from the original CryoSPARC local refinement job.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of half maps reconstructed by RELION 'relion reconstruct'...

Fileemd_39404_half_map_2.map
AnnotationOne of half maps reconstructed by RELION 'relion_reconstruct' command using alignment parameters from the original CryoSPARC local refinement job.
Projections & Slices
AxesZYX

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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: Small Hepatitis B virus surface antigen

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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: Small Hepatitis B virus surface antigen

MacromoleculeName: Small Hepatitis B virus surface antigen / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus ayw/China/Tibet127/2002
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPISNH SPTSCPPTCP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLI PGSSTTSTGP CRTCTTPAQG TSMYPSCCCT KPSDGNCTCI PIPSSWAFGK FLWEWASARF ...String:
MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPISNH SPTSCPPTCP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLI PGSSTTSTGP CRTCTTPAQG TSMYPSCCCT KPSDGNCTCI PIPSSWAFGK FLWEWASARF SWLSLLVPFV QWFVGLSPTV WLSVIWMMWY WGPSLYSILS PFLPLLPIFF CLWVYI

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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: 4527776
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

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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