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- PDB-8w9g: Hepatitis B virus core protein Y132A mutant in complex with CBT-078 -

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Basic information

Entry
Database: PDB / ID: 8w9g
TitleHepatitis B virus core protein Y132A mutant in complex with CBT-078
ComponentsCapsid protein
KeywordsVIRUS 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 subtype adyw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsIwasaki, W. / Katsura, K. / Tomabechi, Y. / Niwa, H. / Ogawa, K. / Kojima, S. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21fk0310112 Japan
CitationJournal: To Be Published
Title: Screening systems for the detection of hepatitis B virus replication and capsid assembly
Authors: Ogawa, K. / Furutani, Y. / Iwasaki, W. / Katsura, K. / Tomabechi, Y. / Kojima, S. / Shirouzu, M.
History
DepositionSep 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Capsid protein
F: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,12012
Polymers104,9216
Non-polymers2,1986
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-33 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.790, 67.660, 85.030
Angle α, β, γ (deg.)68.260, 69.710, 83.010
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17486.916 Da / Num. of mol.: 6 / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus subtype adyw / Strain: isolate United Kingdom/adyw/1979 / Production host: Escherichia coli (E. coli) / References: UniProt: P03147
#2: Chemical
ChemComp-5PT / 2-fluoranyl-N1-(4-fluorophenyl)-N3-(2-methylphenyl)benzene-1,3-dicarboxamide


Mass: 366.361 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H16F2N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.1M sodium citrate (pH 5.7), 13% (v/v) 2-propanol, and 2% PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.5 Å / Num. obs: 37298 / % possible obs: 97.92 % / Redundancy: 3.93 % / Rsym value: 0.106 / Net I/σ(I): 12.12
Reflection shellResolution: 2.6→2.76 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 3485 / Rsym value: 0.706 / % possible all: 93.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0I

5e0i


Resolution: 2.6→43.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.236 1866 -
Rwork0.191 --
obs-37251 97.8 %
Displacement parametersBiso max: 130.6 Å2 / Biso mean: 49.7055 Å2 / Biso min: 19.31 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7087 0 162 191 7440

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