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- PDB-4lmd: Crystal structure of the JCV large t-antigen origin binding domain -

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Basic information

Entry
Database: PDB / ID: 4lmd
TitleCrystal structure of the JCV large t-antigen origin binding domain
ComponentsLarge T antigenLarge tumor antigen
KeywordsHYDROLASE / Origin Binding Domain / DNA Replication
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
CITRATE ANION / Large T antigen
Similarity search - Component
Biological speciesJC polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMeinke, G. / Bohm, A. / Bullock, P.
CitationJournal: Plos Pathog. / Year: 2014
Title: Insights into the Initiation of JC Virus DNA Replication Derived from the Crystal Structure of the T-Antigen Origin Binding Domain.
Authors: Meinke, G. / Phelan, P.J. / Kalekar, R. / Shin, J. / Archambault, J. / Bohm, A. / Bullock, P.A.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9036
Polymers30,3412
Non-polymers5624
Water6,684371
1
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2622
Polymers15,1701
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6414
Polymers15,1701
Non-polymers4703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.067, 37.133, 64.753
Angle α, β, γ (deg.)90.00, 112.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-554-

HOH

DetailsTHE FULL LENGTH T-ANTIGEN FUNCTIONS AS A HEXAMER. THE ISOLATED ORIGIN BINDING DOMAIN (OBD) IS MONOMERIC IN SOLUTION

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Components

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


Mass: 15170.390 Da / Num. of mol.: 2 / Fragment: Origin Binding Domain (unp residues 132-261)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus / Gene: Large T antigen / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P03072, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, 30 % Peg 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Apr 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 51842 / Num. obs: 51172 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 21.17 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4660 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→38.064 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2598 5.13 %random
Rwork0.1667 ---
obs0.1685 50601 97.43 %-
all-51842 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→38.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 38 371 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142332
X-RAY DIFFRACTIONf_angle_d1.5293180
X-RAY DIFFRACTIONf_dihedral_angle_d14.919875
X-RAY DIFFRACTIONf_chiral_restr0.113334
X-RAY DIFFRACTIONf_plane_restr0.008415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.52630.27251180.26821979X-RAY DIFFRACTION78
1.5263-1.55560.25361230.25732249X-RAY DIFFRACTION87
1.5556-1.58740.28161090.24532380X-RAY DIFFRACTION93
1.5874-1.62190.30881640.23912503X-RAY DIFFRACTION98
1.6219-1.65960.2741300.24812526X-RAY DIFFRACTION99
1.6596-1.70110.25011350.21222573X-RAY DIFFRACTION99
1.7011-1.74710.24931330.19672556X-RAY DIFFRACTION99
1.7471-1.79850.24821350.18752576X-RAY DIFFRACTION99
1.7985-1.85660.20451320.17562574X-RAY DIFFRACTION100
1.8566-1.92290.20561280.17392565X-RAY DIFFRACTION100
1.9229-1.99990.1941540.16942574X-RAY DIFFRACTION100
1.9999-2.09090.19911320.1642609X-RAY DIFFRACTION100
2.0909-2.20120.20841510.1582572X-RAY DIFFRACTION100
2.2012-2.33910.20611390.14982599X-RAY DIFFRACTION100
2.3391-2.51960.20671280.16672598X-RAY DIFFRACTION100
2.5196-2.77310.21021230.17332617X-RAY DIFFRACTION100
2.7731-3.17420.20511570.16992618X-RAY DIFFRACTION100
3.1742-3.99850.18471470.14362627X-RAY DIFFRACTION100
3.9985-38.07610.17291600.15362708X-RAY DIFFRACTION100
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)
11.97560.4743-0.481.5709-0.36851.1717-0.03890.09150.04550.00390.0027-0.0832-0.0280.1088-0.00030.1619-0.0043-0.00980.1639-0.00040.132734.739529.606919.8569
21.549-0.7580.25980.5654-0.29911.58620.027-0.0259-0.0326-0.0245-0.03470.03940.0406-0.0124-0.00010.1895-0.00590.0150.16370.00540.171929.202122.055422.0073
31.7944-0.71360.31380.8714-0.32082.25110.0637-0.02190.25880.0139-0.0719-0.0716-0.03020.0104-0.0030.1665-0.0337-0.00710.16510.00520.193556.945739.25960.7462
40.7276-0.5493-0.18470.58280.10120.6692-0.0876-0.2372-0.50880.3053-0.11840.02290.5362-0.0196-0.01270.3165-0.03160.00720.25080.02510.235759.661428.069310.3978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 134:214)
2X-RAY DIFFRACTION2(chain A and resid 215:261)
3X-RAY DIFFRACTION3(chain B and resid 133:229)
4X-RAY DIFFRACTION4(chain B and resid 230:261)

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