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- PDB-5j40: The X-ray structure of JCV Helicase -

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Basic information

Entry
Database: PDB / ID: 5j40
TitleThe X-ray structure of JCV Helicase
ComponentsLarge T antigenLarge tumor antigen
KeywordsHYDROLASE/INHIBITOR / Helicase / hexamer / Zn / ATP / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


suppression by virus of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication origin binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation by virus of host G1/S transition checkpoint / DNA replication / hydrolase activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / 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 (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / Polyomavirus large T antigen C-terminus / Origin of replication binding protein / Zinc finger, large T-antigen D1-type / Large T antigen, polyomavirus, C-terminal / T antigen, Ori-binding ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / Polyomavirus large T antigen C-terminus / Origin of replication binding protein / Zinc finger, large T-antigen D1-type / Large T antigen, polyomavirus, C-terminal / T antigen, Ori-binding / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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

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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)42,7464
Polymers42,3891
Non-polymers3573
Water5,188288
1
A: Large T antigen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)256,47424
Polymers254,3346
Non-polymers2,14018
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 area17630 Å2
ΔGint-172 kcal/mol
Surface area92230 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)109.910, 109.910, 67.890
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 / Large tumor 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 / Plasmid: pET28b.1 / 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 / Zinc


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.79 Å3/Da / Density % sol: 55.95 % / Description: hexameric buttons
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999971 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999971 Å / Relative weight: 1
ReflectionResolution: 2.17→38.972 Å / Num. obs: 22759 / % possible obs: 92 % / Redundancy: 5.7 % / Biso Wilson estimate: 40.78 Å2 / Rsym value: 0.053 / Net I/av σ(I): 11.995 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.17-2.295.60.4461.7194.7
2.29-2.435.70.2912.6193.5
2.43-2.65.70.1864.1193.4
2.6-2.815.70.126.3192.8
2.81-3.085.80.07410.2192.1
3.08-3.445.70.04416.3191.6
3.44-3.975.70.03220.5190
3.97-4.865.60.02722.8188.6
4.86-6.885.60.02920.2187.8
6.88-38.9725.60.02228.1185.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.2data extraction
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→38.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.189
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1182 5.19 %RANDOM
Rwork0.169 ---
obs0.172 22756 91.5 %-
Displacement parametersBiso max: 148.43 Å2 / Biso mean: 45.45 Å2 / Biso min: 21.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.1674 Å20 Å20 Å2
2--3.1674 Å20 Å2
3----6.3349 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2.17→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 31 288 3160
Biso mean--38.58 51.79 -
Num. residues----358
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1034SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes418HARMONIC5
X-RAY DIFFRACTIONt_it2935HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
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_contact3571SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2935HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3984HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion19.49
LS refinement shellResolution: 2.17→2.28 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.275 160 5.41 %
Rwork0.208 2798 -
all-2958 -
obs--90.34 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.37561.4718-0.59443.79051.25751.9320.02510.22520.0988-0.1540.02660.27070.0409-0.2316-0.0518-0.0932-0.00170.0055-0.08170.07310.0388-23.86267.2237-13.2047
22.91990.47620.2281.3581-0.02891.24790.2423-0.0589-0.06970.0374-0.1265-0.2346-0.10290.0656-0.1158-0.0835-0.01260.0606-0.14350.0377-0.0435-31.608319.162115.4486
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|518 - A|628 }A357 - 512
4X-RAY DIFFRACTION2{ A|357 - A|512 A|518 - A|628 }A518 - 628

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