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- PDB-8ymj: Cryo-EM structure of Hepatitis B virus surface antigen subviral p... -

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Basic information

Entry
Database: PDB / ID: 8ymj
TitleCryo-EM structure of Hepatitis B virus surface antigen subviral particle with D2 symmetry
ComponentsIsoform S of Large envelope protein
KeywordsVIRUS LIKE PARTICLE / Surface antigen / Subviral particle
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: 6.6 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
C: Isoform S of Large envelope protein
D: Isoform S of Large envelope protein
E: Isoform S of Large envelope protein
F: Isoform S of Large envelope protein
G: Isoform S of Large envelope protein
H: Isoform S of Large envelope protein
I: Isoform S of Large envelope protein
J: Isoform S of Large envelope protein
K: Isoform S of Large envelope protein
L: Isoform S of Large envelope protein
M: Isoform S of Large envelope protein
N: Isoform S of Large envelope protein
O: Isoform S of Large envelope protein
P: Isoform S of Large envelope protein
Q: Isoform S of Large envelope protein
R: Isoform S of Large envelope protein
S: Isoform S of Large envelope protein
T: Isoform S of Large envelope protein
U: Isoform S of Large envelope protein
V: Isoform S of Large envelope protein
W: Isoform S of Large envelope protein
X: Isoform S of Large envelope protein
Y: Isoform S of Large envelope protein
Z: Isoform S of Large envelope protein
a: Isoform S of Large envelope protein
b: Isoform S of Large envelope protein
c: Isoform S of Large envelope protein
d: Isoform S of Large envelope protein
e: Isoform S of Large envelope protein
f: Isoform S of Large envelope protein
g: Isoform S of Large envelope protein
h: Isoform S of Large envelope protein
i: Isoform S of Large envelope protein
j: Isoform S of Large envelope protein
k: Isoform S of Large envelope protein
l: Isoform S of Large envelope protein
m: Isoform S of Large envelope protein
n: Isoform S of Large envelope protein
o: Isoform S of Large envelope protein
p: Isoform S of Large envelope protein
q: Isoform S of Large envelope protein
r: Isoform S of Large envelope protein
s: Isoform S of Large envelope protein
t: Isoform S of Large envelope protein
u: Isoform S of Large envelope protein
v: Isoform S of Large envelope protein
w: Isoform S of Large envelope protein
x: Isoform S of Large envelope protein
y: Isoform S of Large envelope protein
z: Isoform S of Large envelope protein
1: Isoform S of Large envelope protein
2: Isoform S of Large envelope protein
3: Isoform S of Large envelope protein
4: Isoform S of Large envelope protein
5: Isoform S of Large envelope protein
6: Isoform S of Large envelope protein
7: Isoform S of Large envelope protein
8: Isoform S of Large envelope protein
9: Isoform S of Large envelope protein
0: Isoform S of Large envelope protein
AA: Isoform S of Large envelope protein
AB: Isoform S of Large envelope protein
AC: Isoform S of Large envelope protein
AD: Isoform S of Large envelope protein
AE: Isoform S of Large envelope protein
AF: Isoform S of Large envelope protein
AG: Isoform S of Large envelope protein
AH: Isoform S of Large envelope protein
AI: Isoform S of Large envelope protein
AJ: Isoform S of Large envelope protein
AK: Isoform S of Large envelope protein
AL: Isoform S of Large envelope protein
AM: Isoform S of Large envelope protein
AN: Isoform S of Large envelope protein
AO: Isoform S of Large envelope protein
AP: Isoform S of Large envelope protein
AQ: Isoform S of Large envelope protein
AR: Isoform S of Large envelope protein


Theoretical massNumber of molelcules
Total (without water)2,032,64580
Polymers2,032,64580
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • 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.: 80
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
IDNameVersionCategoryFitting-ID
1RELIONparticle selection
2SerialEMimage acquisition
7UCSF Chimera1.16model fitting1
12cryoSPARC3D reconstruction
14iMODFIT1.51model fitting2
15PHENIX1.20.1_4487:model refinement2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10324877
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113208 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1RIGID BODY FITREAL
2FLEXIBLE FITREAL
Atomic model building
ID 3D fitting-IDSource nameType
11AlphaFoldin silico model
22AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003107142
ELECTRON MICROSCOPYf_angle_d0.633149006
ELECTRON MICROSCOPYf_dihedral_angle_d5.30818384
ELECTRON MICROSCOPYf_chiral_restr0.04217920
ELECTRON MICROSCOPYf_plane_restr0.00520112

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