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- PDB-5cyn: JC Virus large T-antigen origin binding domain F258L mutant -

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Basic information

Entry
Database: PDB / ID: 5cyn
TitleJC Virus large T-antigen origin binding domain F258L mutant
ComponentsLarge T antigenLarge tumor antigen
Keywordsviral protein / dna binding protein / DNA binding domain / origin binding domain
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / metal ion binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / 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 ...Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / 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 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMeinke, G. / Bohm, A. / Bullock, P.A.
CitationJournal: Plos Pathog. / Year: 2016
Title: Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains.
Authors: Meinke, G. / Phelan, P.J. / Shin, J. / Gagnon, D. / Archambault, J. / Bohm, A. / Bullock, P.A.
History
DepositionJul 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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)15,0542
Polymers14,9921
Non-polymers621
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.540, 103.540, 34.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Large T antigen / Large tumor antigen / LT-AG


Mass: 14992.244 Da / Num. of mol.: 1 / Fragment: unp residues 132-261 / Mutation: F258L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Plasmid: pGEX1lT / Details (production host): GST fusion / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Rosetta (DE3)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25-35% Peg 6000 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 5183 / Num. obs: 5163 / % possible obs: 99.6 % / Redundancy: 15.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 37.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LIF
Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 23.55 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22747 263 5.1 %RANDOM
Rwork0.1952 ---
obs0.19682 4927 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 4 7 1043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191062
X-RAY DIFFRACTIONr_bond_other_d0.0020.021010
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9371430
X-RAY DIFFRACTIONr_angle_other_deg0.85732319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8275126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32123.33351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.397155
X-RAY DIFFRACTIONr_chiral_restr0.0680.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02271
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_it0.6174.086507
X-RAY DIFFRACTIONr_mcbond_other0.6184.083506
X-RAY DIFFRACTIONr_mcangle_it1.0846.123632
X-RAY DIFFRACTIONr_mcangle_other1.0836.127633
X-RAY DIFFRACTIONr_scbond_it0.4274.148555
X-RAY DIFFRACTIONr_scbond_other0.4244.148555
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.776.195799
X-RAY DIFFRACTIONr_long_range_B_refined2.28232.0981140
X-RAY DIFFRACTIONr_long_range_B_other2.26732.0941140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 17 -
Rwork0.248 349 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.792 Å / Origin y: -8.813 Å / Origin z: 0.953 Å
111213212223313233
T0.2005 Å20.1192 Å2-0.0219 Å2-0.0936 Å2-0.0596 Å2--0.1196 Å2
L7.9719 °2-3.3605 °2-1.1753 °2-7.4036 °2-1.0879 °2--4.4097 °2
S0.2356 Å °0.1763 Å °0.2642 Å °-0.2314 Å °-0.1041 Å °-0.3565 Å °-0.7433 Å °-0.3174 Å °-0.1314 Å °

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