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- PDB-8i71: Hepatitis B virus core protein Y132A mutant in complex with Linve... -

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Basic information

Entry
Database: PDB / ID: 8i71
TitleHepatitis B virus core protein Y132A mutant in complex with Linvencorvir (RG7907), a Hepatitis B Virus (HBV) Core Protein Allosteric Modulator (CpAM)
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / capsid assembly inhibitor / ANTIVIRAL PROTEIN
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
ISOPROPYL ALCOHOL / Chem-OTI / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus subtype adyw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhou, Z. / Xu, Z.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of Linvencorvir (RG7907), a Hepatitis B Virus Core Protein Allosteric Modulator, for the Treatment of Chronic HBV Infection.
Authors: Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Shi, H. / Zhou, M. / Zhang, Z. / Kou, B. / Hu, T. / Zhou, Z. / Xu, Z. / Zhou, X. / Zhou, Y. / Tian, X. / Yang, G. / Young, J.A.T. / Qiu, H. / ...Authors: Zhang, W. / Guo, L. / Liu, H. / Wu, G. / Shi, H. / Zhou, M. / Zhang, Z. / Kou, B. / Hu, T. / Zhou, Z. / Xu, Z. / Zhou, X. / Zhou, Y. / Tian, X. / Yang, G. / Young, J.A.T. / Qiu, H. / Ottaviani, G. / Xie, J. / Mayweg, A.V. / Shen, H.C. / Zhu, W.
History
DepositionJan 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)109,67831
Polymers104,9216
Non-polymers4,75725
Water12,665703
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19480 Å2
ΔGint-136 kcal/mol
Surface area45250 Å2
Unit cell
Length a, b, c (Å)64.392, 67.565, 86.246
Angle α, β, γ (deg.)68.60, 69.81, 83.87
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P03147

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Non-polymers , 6 types, 728 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-OTI / 3-[(8~{a}~{S})-7-[[5-ethoxycarbonyl-4-(3-fluoranyl-2-methyl-phenyl)-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-3-oxidanylidene-5,6,8,8~{a}-tetrahydro-1~{H}-imidazo[1,5-a]pyrazin-2-yl]-2,2-dimethyl-propanoic acid / Linvencorvir


Mass: 598.689 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H35FN6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 703 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM citrate, 21%(vol/vol) isopropanol, 1%(W/V) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 650539 / % possible obs: 95.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.2
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.811 / Num. unique obs: 160629

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Processing

Software
NameVersionClassification
PHENIX1.1refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.513 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 3952 2.47 %
Rwork0.1549 --
obs0.1558 159928 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 321 703 8248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117860
X-RAY DIFFRACTIONf_angle_d0.96610802
X-RAY DIFFRACTIONf_dihedral_angle_d17.3064523
X-RAY DIFFRACTIONf_chiral_restr0.0531189
X-RAY DIFFRACTIONf_plane_restr0.0071359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61950.32091280.32485095X-RAY DIFFRACTION88
1.6195-1.640.32071430.31145338X-RAY DIFFRACTION91
1.64-1.66160.29861270.30335417X-RAY DIFFRACTION92
1.6616-1.68440.30261360.2815431X-RAY DIFFRACTION94
1.6844-1.70840.29511440.2695426X-RAY DIFFRACTION94
1.7084-1.73390.25541630.25295598X-RAY DIFFRACTION95
1.7339-1.7610.27611350.23155575X-RAY DIFFRACTION95
1.761-1.78990.24731240.22255565X-RAY DIFFRACTION95
1.7899-1.82070.23011520.21195561X-RAY DIFFRACTION96
1.8207-1.85380.23591350.19735530X-RAY DIFFRACTION95
1.8538-1.88950.2051490.18025592X-RAY DIFFRACTION95
1.8895-1.92810.22141370.17695615X-RAY DIFFRACTION96
1.9281-1.970.18321420.16725594X-RAY DIFFRACTION96
1.97-2.01580.19921660.16275572X-RAY DIFFRACTION96
2.0158-2.06620.19031310.15295633X-RAY DIFFRACTION96
2.0662-2.12210.19761410.15065598X-RAY DIFFRACTION97
2.1221-2.18450.20481360.13655650X-RAY DIFFRACTION96
2.1845-2.2550.19231400.14075670X-RAY DIFFRACTION96
2.255-2.33560.15631400.135635X-RAY DIFFRACTION97
2.3356-2.42910.18011490.13215626X-RAY DIFFRACTION97
2.4291-2.53960.19891470.14665654X-RAY DIFFRACTION97
2.5396-2.67340.1951320.15245688X-RAY DIFFRACTION97
2.6734-2.84080.20031510.1535663X-RAY DIFFRACTION97
2.8408-3.060.18341400.15025625X-RAY DIFFRACTION96
3.06-3.36770.18011390.14465604X-RAY DIFFRACTION96
3.3677-3.85440.17731390.13285654X-RAY DIFFRACTION97
3.8544-4.85380.15951460.1215803X-RAY DIFFRACTION99
4.8538-33.5130.18281400.15655564X-RAY DIFFRACTION95

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