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- PDB-5e0i: Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in c... -

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Basic information

Entry
Database: PDB / ID: 5e0i
TitleCrystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2 at 1.95A resolution
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / NVR10-001E2
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 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
Chem-5J6 / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus genotype D subtype adw
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLukacs, C.M. / Abendroth, J. / Klumpp, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: High-resolution crystal structure of a hepatitis B virus replication inhibitor bound to the viral core protein.
Authors: Klumpp, K. / Lam, A.M. / Lukacs, C. / Vogel, R. / Ren, S. / Espiritu, C. / Baydo, R. / Atkins, K. / Abendroth, J. / Liao, G. / Efimov, A. / Hartman, G. / Flores, O.A.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)109,08912
Polymers106,1296
Non-polymers2,9606
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15440 Å2
ΔGint-129 kcal/mol
Surface area40500 Å2
2
A: Capsid protein
F: Capsid protein
hetero molecules

D: Capsid protein
E: Capsid protein
hetero molecules

B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,08912
Polymers106,1296
Non-polymers2,9606
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area9240 Å2
ΔGint-65 kcal/mol
Surface area46700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.600, 88.170, 102.250
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 17688.203 Da / Num. of mol.: 6 / Fragment: HBV CAPSID Y132A / Mutation: Y132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus genotype D subtype adw
Strain: isolate United Kingdom/adyw/1979 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03147
#2: Chemical
ChemComp-5J6 / methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate / NVR10-001E2


Mass: 493.349 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H18BrFN4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 3.36 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M AMMONIUM CITRATE/CITRIC ACID PH 6.5, 9% ISOPROPANOL, 10% PEG 3350, 10% MPD, VAPOR DIFFUSION, TEMPERATURE 293K
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 14, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 96089 / Num. obs: 95947 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.74 % / Biso Wilson estimate: 26.35 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.35
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.77 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BMG

4bmg


Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.92 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.252 4810 5 %RANDOM
Rwork0.219 ---
obs0.221 95947 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20.52 Å2
2---1.79 Å20 Å2
3---2.79 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 180 440 7484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197324
X-RAY DIFFRACTIONr_bond_other_d0.0010.026624
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.97110059
X-RAY DIFFRACTIONr_angle_other_deg0.9282.99615218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64223.041296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.738151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6131538
X-RAY DIFFRACTIONr_chiral_restr0.0960.21140
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.653534
X-RAY DIFFRACTIONr_mcbond_other1.0581.6493533
X-RAY DIFFRACTIONr_mcangle_it1.6982.4554400
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 379 -
Rwork0.254 6696 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.64340.2961-0.17121.1881-0.08780.1145-0.02920.0732-0.07640.02160.02220.0206-0.05790.06660.0070.0401-0.0356-0.00690.0555-0.00690.0924154.3008-51.9128127.1777
23.71840.35890.13691.3935-0.03150.1014-0.03080.06350.03010.04940.0203-0.03430.0567-0.06130.01050.0437-0.0360.00670.04720.00590.0899179.5925-41.1564127.5008
32.9005-1.56020.50253.8475-0.24450.12580.05040.0024-0.00340.003-0.085-0.0275-0.0038-0.05470.03460.00960.02270.01180.0877-0.01440.1297178.3672-11.1283126.1698
43.034-1.5181-0.49473.67690.19570.14780.0375-0.0099-0.0486-0.0015-0.08050.02450.0190.07450.0430.01690.0314-0.01610.08320.01540.1292155.75836.3985126.0364
51.87930.85010.00174.13290.44620.0814-0.0382-0.0820.0328-0.08850.02430.00330.03620.02370.01390.07810.0247-0.00310.02090.01060.1059131.0587-9.9561126.0647
62.04051.1542-0.02274.27-0.45980.0709-0.0417-0.0095-0.0489-0.14010.0301-0.0064-0.0198-0.01710.01160.08660.0257-0.00550.0196-0.01420.0899126.7147-39.108125.1712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 500
2X-RAY DIFFRACTION2B0 - 500
3X-RAY DIFFRACTION3C0 - 500
4X-RAY DIFFRACTION4D1 - 500
5X-RAY DIFFRACTION5E0 - 500
6X-RAY DIFFRACTION6F0 - 500

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