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- PDB-4fgn: Crystal structure of the SV40 large T-antigen origin bining domai... -

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Basic information

Entry
Database: PDB / ID: 4fgn
TitleCrystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA
Components
  • (Site I DNA) x 2
  • Large T antigen
KeywordsDNA BINDING PROTEIN/DNA / origin binding domain / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / single-stranded DNA binding / double-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA replication / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / 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 ...Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / 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 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMeinke, G. / Bohm, A. / Bullock, P.A.
CitationJournal: J.Virol. / Year: 2013
Title: Analysis of the Costructure of the Simian Virus 40 T-Antigen Origin Binding Domain with Site I Reveals a Correlation between GAGGC Spacing and Spiral Assembly.
Authors: Meinke, G. / Phelan, P.J. / Harrison, C.J. / Bullock, P.A.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
Z: Site I DNA
Y: Site I DNA


Theoretical massNumber of molelcules
Total (without water)44,6034
Polymers44,6034
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-34 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.604, 139.672, 132.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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Components

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


Mass: 15240.476 Da / Num. of mol.: 2 / Fragment: origin binding domain, UNP residues 131-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3)
References: UniProt: P03070, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain Site I DNA


Mass: 6963.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is termed Site 1 in SV40 / Source: (synth.) Simian virus 40
#3: DNA chain Site I DNA


Mass: 7158.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is from sv40 site I / Source: (synth.) Simian virus 40
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, .2M ammonium sulfate, 30 % Peg 4000, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 9304 / % possible obs: 100 % / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NTC

2ntc


Resolution: 3.2→47.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 73.091 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.267 444 4.8 %RANDOM
Rwork0.188 ---
obs0.191 8841 99.8 %-
all-9305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 137.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 937 0 3 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0173132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.7374434
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2245248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38423.06198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.7515345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1341510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212062
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 29 -
Rwork0.302 563 -
obs--97.69 %
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)
14.3163-2.8324-1.074314.33322.366611.86250.0745-0.2827-0.97940.8123-0.71720.64960.5555-0.35030.64270.3479-0.03020.23840.603-0.06790.82321.559442.2545-0.2878
210.87222.96351.324111.11750.23693.73420.9076-0.6183-0.5681-0.2245-0.73371.44211.6383-1.9481-0.17381.2112-0.4074-0.43741.5418-0.19610.71153.13835.6793-17.5268
34.5856-5.0544-0.71618.9033.24123.24170.63740.31980.9739-1.2909-0.4605-1.7934-0.32160.3427-0.17691.05340.27110.16180.6879-0.04190.764917.687627.3756-20.0936
42.5926-2.63391.44694.07130.47064.19540.90310.58190.0307-1.4441-0.77360.2976-0.27650.1121-0.12950.98320.20060.23390.6251-0.05330.781416.444729.9636-20.6853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 258
2X-RAY DIFFRACTION2B134 - 257
3X-RAY DIFFRACTION3Z1 - 23
4X-RAY DIFFRACTION4Y1 - 23

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