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- EMDB-7294: Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-7294
TitleCryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA
Map dataA Hepatitis B virus capsid with T=4 symmetry, bound to HAP-TAMRA. HAP-TAMRA is a fluorescent probe derived from the Heteroaryldihydropyrimidine (HAP) class of capsid-directed antivirals.
SampleHepatitis B virus T=4 capsid != Hepatitis B virus genotype D subtype adw

Hepatitis B virus T=4 capsid

  • Virus: Hepatitis B virus genotype D subtype adw
    • Protein or peptide: Capsid protein
  • Ligand: Heteroaryldihydropyrimidine tetramethylrodamine
Keywordscapsid / CpAM / antiviral / fluorescent / 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: 4.0 Å
AuthorsSchlicksup C / Wang JC
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: Elife / Year: 2018
Title: Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids.
Authors: Christopher John Schlicksup / Joseph Che-Yen Wang / Samson Francis / Balasubramanian Venkatakrishnan / William W Turner / Michael VanNieuwenhze / Adam Zlotnick /
Abstract: Defining mechanisms of direct-acting antivirals facilitates drug development and our understanding of virus function. Heteroaryldihydropyrimidines (HAPs) inappropriately activate assembly of ...Defining mechanisms of direct-acting antivirals facilitates drug development and our understanding of virus function. Heteroaryldihydropyrimidines (HAPs) inappropriately activate assembly of hepatitis B virus (HBV) core protein (Cp), suppressing formation of virions. We examined a fluorophore-labeled HAP, HAP-TAMRA. HAP-TAMRA induced Cp assembly and also bound pre-assembled capsids. Kinetic and spectroscopic studies imply that HAP-binding sites are usually not available but are bound cooperatively. Using cryo-EM, we observed that HAP-TAMRA asymmetrically deformed capsids, creating a heterogeneous array of sharp angles, flat regions, and outright breaks. To achieve high resolution reconstruction (<4 Å), we introduced a disulfide crosslink that rescued particle symmetry. We deduced that HAP-TAMRA caused quasi-sixfold vertices to become flatter and fivefold more angular. This transition led to asymmetric faceting. That a disordered crosslink could rescue symmetry implies that capsids have tensegrity properties. Capsid distortion and disruption is a new mechanism by which molecules like the HAPs can block HBV infection.
History
DepositionDec 12, 2017-
Header (metadata) releaseFeb 7, 2018-
Map releaseFeb 7, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bvf
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bvf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7294.png

Downloads & links

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Map

FileDownload / File: emd_7294.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA Hepatitis B virus capsid with T=4 symmetry, bound to HAP-TAMRA. HAP-TAMRA is a fluorescent probe derived from the Heteroaryldihydropyrimidine (HAP) class of capsid-directed antivirals.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 380 pix.
= 488.3 Å		1.29 Å/pix.
x 380 pix.
= 488.3 Å		1.29 Å/pix.
x 380 pix.
= 488.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.056519054 - 0.1568575
Average (Standard dev.)0.00042570985 (±0.01004744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 488.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2851.2851.285
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z488.300488.300488.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0570.1570.000

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Supplemental data

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Sample components

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Entire : Hepatitis B virus T=4 capsid

EntireName: Hepatitis B virus T=4 capsid
Components
  • Virus: Hepatitis B virus genotype D subtype adw
    • Protein or peptide: Capsid protein
  • Ligand: Heteroaryldihydropyrimidine tetramethylrodamine

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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: Heteroaryldihydropyrimidine tetramethylrodamine

MacromoleculeName: Heteroaryldihydropyrimidine tetramethylrodamine / type: ligand / ID: 2 / Number of copies: 2 / Formula: E9D
Molecular weightTheoretical: 939.428 Da
Chemical component information

ChemComp-E9D:
Heteroaryldihydropyrimidine tetramethylrodamine

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Software - details: Automated B-factor Sharpening / Number images used: 16008
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:

5d7y


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-6bvf:
Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA

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