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- PDB-2itl: The origin binding domain of the SV40 large T antigen bound to th... -

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Basic information

Entry
Database: PDB / ID: 2itl
TitleThe origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp)
Components
  • (24-nt PEN element of the SV40 DNA origin) x 2
  • large T antigen
KeywordsDNA binding protein/DNA / DNA binding protein / 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 / helicase activity / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification ...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 / helicase activity / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA replication / hydrolase activity / 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 / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBochkareva, E. / Seitova, A. / Bochkarev, A.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA
Authors: Bochkareva, E. / Martynowski, D. / Seitova, A. / Bochkarev, A.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 30, 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
W: 24-nt PEN element of the SV40 DNA origin
C: 24-nt PEN element of the SV40 DNA origin
A: large T antigen
B: large T antigen


Theoretical massNumber of molelcules
Total (without water)45,5174
Polymers45,5174
Non-polymers00
Water5,531307
1
W: 24-nt PEN element of the SV40 DNA origin
C: 24-nt PEN element of the SV40 DNA origin
A: large T antigen
B: large T antigen

W: 24-nt PEN element of the SV40 DNA origin
C: 24-nt PEN element of the SV40 DNA origin
A: large T antigen
B: large T antigen


Theoretical massNumber of molelcules
Total (without water)91,0348
Polymers91,0348
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)83.196, 64.096, 79.177
Angle α, β, γ (deg.)90.00, 120.69, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dsDNA fragment bound by four OBDs

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Components

#1: DNA chain 24-nt PEN element of the SV40 DNA origin


Mass: 7397.742 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 24-nt PEN element of the SV40 DNA origin


Mass: 7357.718 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein large T antigen


Mass: 15380.704 Da / Num. of mol.: 2 / Fragment: Origin binding domain (residues 131-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Strain: 776 / Gene: large T antigen / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P03070, UniProt: Q98ZP7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM di-ammonium hydrogen citrate, 20% PEG 3000, and 10 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1di-ammonium hydrogen citrate11
2PEG 300011
3MgCl211
4di-ammonium hydrogen citrate12
5PEG 300012
6MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9176 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9176 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. all: 42961 / Num. obs: 42961 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.062 / Net I/σ(I): 23.8
Reflection shellResolution: 1.65→1.71 Å / Num. unique all: 4204 / Rsym value: 0.213 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CHESSF1data collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPR

2ipr


Resolution: 1.65→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.384 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25061 2161 5 %RANDOM
Rwork0.2013 ---
obs0.20378 40799 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.282 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 979 0 307 3207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.462.2063507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.17622.64487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15915345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0231510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021713
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21039
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21691
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2631.51201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04521911
X-RAY DIFFRACTIONr_scbond_it2.77431663
X-RAY DIFFRACTIONr_scangle_it3.34.51596
X-RAY DIFFRACTIONr_rigid_bond_restr3.01232864
X-RAY DIFFRACTIONr_sphericity_free5.1123322
X-RAY DIFFRACTIONr_sphericity_bonded4.05532409
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 170 -
Rwork0.25 2925 -
obs--97.02 %

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