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- PDB-8uyz: HBV Cp149 capsid protein (HBV dimer co-assembled with triton X-100) -

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Basic information

Entry
Database: PDB / ID: 8uyz
TitleHBV Cp149 capsid protein (HBV dimer co-assembled with triton X-100)
ComponentsCapsid protein
KeywordsVIRUS / HBV / Hepatitis B / Capsid / Core Protein / Cp149
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBianchini, E.N. / Wang, J.C.Y. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI173104 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI043453 United States
CitationJournal: To Be Published
Title: Structural Insights into Capsid Conformation and Dynamics: Cryo-EM Structures of HBV Capsids from HEK-293T Cells
Authors: Bianchini, E.N. / Liu, H. / Cai, Y. / Shanklin, J. / Hu, J. / Wang, J.C.Y.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)84,3284
Polymers84,3284
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,059,706240
Polymers5,059,706240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
x 5


  • icosahedral pentamer
  • 422 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)421,64220
Polymers421,64220
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 506 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)505,97124
Polymers505,97124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Capsid protein / Core antigen / Core protein / HBcAg / p21.5


Mass: 21082.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus
Gene: pre-c/core, C, core, pre-C/C, PreC, preC, preC/C, precore-core, HBVgp4
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89656
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 / Type: VIRUS
Details: Recombinant C-terminal truncated HBV capsid protein was expressed in E. coli
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 4 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis B virus
Source (recombinant)Organism: Escherichia coli (E. coli) / Cell: BL21-DE3
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: capsid protein / Diameter: 340 nm / Triangulation number (T number): 4
Buffer solutionpH: 7.5 / Details: 500 mM NaCl, 50 mM HEPES, pH 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 64000 X / Nominal defocus max: 6800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2007
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4RELION3.1CTF correction
7UCSF ChimeraXmodel fitting
9ISOLDEmodel refinement
10PHENIXmodel refinement
11Cootmodel refinement
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9116 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1QGT

1qgt


Accession code: 1QGT / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0194685
ELECTRON MICROSCOPYf_angle_d1.3996423
ELECTRON MICROSCOPYf_dihedral_angle_d4.191618
ELECTRON MICROSCOPYf_chiral_restr0.037732
ELECTRON MICROSCOPYf_plane_restr0.005814

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