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- PDB-6bvn: Cryo-EM Structure of Hepatitis B virus T=3 capsid in complex with... -

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Basic information

Entry
Database: PDB / ID: 6bvn
TitleCryo-EM Structure of Hepatitis B virus T=3 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / capsid / CpAM / antiviral / fluorescent
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 cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / identical protein binding
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Heteroaryldihydropyrimidine tetramethylrodamine / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype D subtype adw
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSchlicksup, C. / Wang, J.C. / Zlotnick, A.
Funding support United States, 1items
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 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 2.0Apr 13, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
C: Capsid protein
B: Capsid protein
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3134
Polymers50,3733
Non-polymers9391
Water0
1
C: Capsid protein
B: Capsid protein
A: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)3,078,764240
Polymers3,022,399180
Non-polymers56,36660
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
C: Capsid protein
B: Capsid protein
A: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 257 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)256,56420
Polymers251,86715
Non-polymers4,6975
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Capsid protein
B: Capsid protein
A: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 308 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)307,87624
Polymers302,24018
Non-polymers5,6376
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 / Capsid / Core antigen / Core protein / HBcAg / p21.5


Mass: 16791.104 Da / Num. of mol.: 3 / Fragment: UNP residues 1-149 / Mutation: C48A, C61A, C107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype D subtype adw
Production host: Escherichia coli (E. coli) / References: UniProt: P03147
#2: Chemical ChemComp-E9D / Heteroaryldihydropyrimidine tetramethylrodamine / HAP-TAMRA


Mass: 939.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H48ClFN8O7

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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 T=3 capsid / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Hepatitis B virus genotype D subtype adw / Strain: isolate United Kingdom/adyw/1979
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2300 mMSodium ChlorideNaClSodium chloride1
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 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 FIELDBright-field microscopy
Image recordingElectron dose: 33 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 679

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Processing

EM software
IDNameVersionCategoryDetails
4CTFFIND4.1CTF correction
7Coot0.8.7model fitting
12RELION2.13D reconstructionAutomated B-factor Sharpening
13PHENIX1.11model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 24823
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16008 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation Coefficient
Atomic model buildingPDB-ID: 5D7Y

5d7y


Pdb chain-ID: A / Pdb chain residue range: 1-143

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