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- EMDB-21653: Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-21653
TitleCryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the antiviral molecule DBT1
Map dataHBV capsid in complex with the antiviral molecule DBT1. Icosahedral averaging imposed.
Sample
  • Virus: Hepatitis B virus genotype D subtype adw
    • Protein or peptide: Capsid protein
  • Ligand: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide
Keywordscapsid / antiviral / HBV / VIRUS LIKE PARTICLE
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 / identical protein binding
Similarity search - Function
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Biological speciesHepatitis B virus genotype D subtype adw
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSchlicksup C / Laughlin P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI067417 United States
CitationJournal: ACS Chem Biol / Year: 2020
Title: Local Stabilization of Subunit-Subunit Contacts Causes Global Destabilization of Hepatitis B Virus Capsids.
Authors: Christopher John Schlicksup / Patrick Laughlin / Steven Dunkelbarger / Joseph Che-Yen Wang / Adam Zlotnick /
Abstract: Development of antiviral molecules that bind virion is a strategy that remains in its infancy, and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a ...Development of antiviral molecules that bind virion is a strategy that remains in its infancy, and the details of their mechanisms are poorly understood. Here we investigate the behavior of DBT1, a dibenzothiazepine that specifically interacts with the capsid protein of hepatitis B virus (HBV). We found that DBT1 stabilizes protein-protein interaction, accelerates capsid assembly, and can induce formation of aberrant particles. Paradoxically, DBT1 can cause preformed capsids to dissociate. These activities may lead to (i) assembly of empty and defective capsids, inhibiting formation of new virus, and (ii) disruption of mature viruses, which are metastable, to inhibit new infection. Using cryo-electron microscopy, we observed that DBT1 led to asymmetric capsids where well-defined DBT1 density was bound at all intersubunit contacts. These results suggest that DBT1 can support assembly by increasing buried surface area but induce disassembly of metastable capsids by favoring asymmetry to induce structural defects.
History
DepositionApr 3, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wfs
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wfs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21653.png

Downloads & links

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Map

FileDownload / File: emd_21653.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHBV capsid in complex with the antiviral molecule DBT1. Icosahedral averaging imposed.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 640 pix.
= 416. Å		0.65 Å/pix.
x 640 pix.
= 416. Å		0.65 Å/pix.
x 640 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.003
Minimum - Maximum-0.0039472342 - 0.010579796
Average (Standard dev.)0.00018753625 (±0.0008393019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-319-319-319
Dimensions640640640
Spacing640640640
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-319-319-319
NC/NR/NS640640640
D min/max/mean-0.0040.0110.000

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Supplemental data

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Mask #1

Fileemd_21653_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hepatitis B virus genotype D subtype adw

EntireName: Hepatitis B virus genotype D subtype adw
Components
  • Virus: Hepatitis B virus genotype D subtype adw
    • Protein or peptide: Capsid protein
  • Ligand: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide

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Supramolecule #1: Hepatitis B virus genotype D subtype adw

SupramoleculeName: Hepatitis B virus genotype D subtype adw / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10419 / Sci species name: Hepatitis B virus genotype D subtype adw / Sci species strain: isolate United Kingdom/adyw/1979 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis B virus genotype D subtype adw
Molecular weightTheoretical: 16.791104 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTAAALYRD ALESPEHASP HHTALRQAIL AWGDLMTLAT WVGTNLEDPA SRDLVVSYV NTNVGLKFRQ LLWFHISALT FGRETVLEYL VSFGVWIRTP PAYRPPNAPI LSTLPETTVV C

UniProtKB: Capsid protein

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Macromolecule #2: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1...

MacromoleculeName: 11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide
type: ligand / ID: 2 / Number of copies: 4 / Formula: U0A
Molecular weightTheoretical: 453.534 Da
Chemical component information

ChemComp-U0A:
11-oxo-N-[2-(4-sulfamoylphenyl)ethyl]-10,11-dihydrodibenzo[b,f][1,4]thiazepine-8-carboxamide

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium Chloride
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 679 / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 24823
Startup modelType of model: NONE / Details: A spherical volume with a diameter of 35 nm
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Software - details: Automated B-factor Sharpening / Number images used: 11080
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bvf


Chain - Chain ID: A / Chain - Residue range: 1-143 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation Coefficient
Output model

PDB-6wfs:
Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the antiviral molecule DBT1

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