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- PDB-5j47: The X-ray structure of Inhibitor Bound to JCV Helicase -

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Basic information

Entry
Database: PDB / ID: 5j47
TitleThe X-ray structure of Inhibitor Bound to JCV Helicase
ComponentsLarge T antigen
KeywordsHYDROLASE/INHIBITOR / Helicase / hexamer / Zn / ATP / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / DNA replication / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / DNA replication / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6JJ / Large T antigen
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 Å
AuthorsTer Haar, E.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Fragment-Based Discovery of Dual JC Virus and BK Virus Helicase Inhibitors.
Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / ...Authors: Bonafoux, D. / Nanthakumar, S. / Bandarage, U.K. / Memmott, C. / Lowe, D. / Aronov, A.M. / Bhisetti, G.R. / Bonanno, K.C. / Coll, J. / Leeman, J. / Lepre, C.A. / Lu, F. / Perola, E. / Rijnbrand, R. / Taylor, W.P. / Wilson, D. / Zhou, Y. / Zwahlen, J. / Ter Haar, E.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9444
Polymers42,3891
Non-polymers5553
Water6,305350
1
A: Large T antigen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)257,66424
Polymers254,3346
Non-polymers3,33018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area15270 Å2
ΔGint-50 kcal/mol
Surface area94010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.710, 110.710, 67.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Large T antigen / LT-AG


Mass: 42388.984 Da / Num. of mol.: 1 / Fragment: UNP residues 261-628
Mutation: E280A, D295N, N299A, Q301A, Q302A, K304A, K305A, E307A, K308A, K309A, I354L, D408E, R624A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Production host: Escherichia coli (E. coli)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-6JJ / 6-(2-phenoxyphenyl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole


Mass: 294.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10N4OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: hexagonal button
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25-30% Peg400, 0.1 M LiSO4, 0.1M HEPES (pH 7.0), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999971 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999971 Å / Relative weight: 1
ReflectionResolution: 1.99→31.96 Å / Num. obs: 31960 / % possible obs: 98.12 % / Redundancy: 5 % / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
SCALACCP4_3.3.20data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.99→31.96 Å / Cor.coef. Fo:Fc: 0.9596 / Cor.coef. Fo:Fc free: 0.9474 / SU R Cruickshank DPI: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.161 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1620 5.07 %RANDOM
Rwork0.1832 ---
obs0.1851 31960 98.12 %-
Displacement parametersBiso max: 126.06 Å2 / Biso mean: 44.78 Å2 / Biso min: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.0973 Å20 Å20 Å2
2--0.0973 Å20 Å2
3----0.1946 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: final / Resolution: 1.99→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 47 350 3251
Biso mean--43.84 50.25 -
Num. residues----360
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1041SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it2968HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion374SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3609SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2968HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4029HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion19.45
LS refinement shellResolution: 1.99→2.06 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2537 155 5.21 %
Rwork0.1899 2821 -
all0.1931 2976 -
obs--99.23 %
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)
12.16140.753-0.88975.01161.02651.16080.07430.25030.1261-0.1118-0.01510.25960.0325-0.163-0.0591-0.1580.00970.0028-0.12140.08130.1824-23.9677.2293-13.1755
22.95710.53380.03041.3011-0.01070.76780.177-0.1542-0.09980.1113-0.1113-0.1775-0.0190.0828-0.0656-0.2001-0.01510.0159-0.20710.04990.2198-31.714919.453415.3559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A1
2X-RAY DIFFRACTION1{ A|701 - A|701 A|266 - A|356 }A266 - 356
3X-RAY DIFFRACTION2{ A|357 - A|512 A|516 - A|627 }A357 - 512
4X-RAY DIFFRACTION2{ A|357 - A|512 A|516 - A|627 }A516 - 627

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