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- PDB-2nl8: The origin binding domain of the SV40 large T antigen bound non s... -

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Basic information

Entry
Database: PDB / ID: 2nl8
TitleThe origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)
Components
  • 18-nt PEN element of the SV40 DNA origin
  • large T antigenLarge tumor 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 unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / identical protein 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
DNA / DNA (> 10) / Large T antigen / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMartynowski, D. / Bochkareva, E. / 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 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: 18-nt PEN element of the SV40 DNA origin
A: large T antigen


Theoretical massNumber of molelcules
Total (without water)20,8422
Polymers20,8422
Non-polymers00
Water1,47782
1
W: 18-nt PEN element of the SV40 DNA origin
A: large T antigen

W: 18-nt PEN element of the SV40 DNA origin
A: large T antigen


Theoretical massNumber of molelcules
Total (without water)41,6844
Polymers41,6844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)43.870, 43.870, 238.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 18-nt PEN element of the SV40 DNA origin


Mass: 5477.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: P2 pentamer replaced with ATCAT
#2: Protein large T antigen / Large tumor antigen


Mass: 15364.638 Da / Num. of mol.: 1 / Fragment: Origin binding domain (residues 131-259) / Mutation: CYS216SER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM NaAcetate, 20% PEG 3000 + 4% PEG 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaAcetate11
2PEG 300011
3PEG 60011
4NaAcetate12
5PEG 300012
6PEG 60012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 26, 2004 / Details: mirrors
RadiationMonochromator: Rigaku/MSC green optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 11307 / Num. obs: 11307 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.044 / Net I/σ(I): 18.1
Reflection shellResolution: 2.25→2.33 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.439 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
MOLREPphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IPR

1ipr


Resolution: 2.3→19.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.599 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29895 518 4.9 %RANDOM
Rwork0.23682 ---
obs0.23999 10057 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.138 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 363 0 82 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1912.2861958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6875116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01322.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28415172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.005155
X-RAY DIFFRACTIONr_chiral_restr0.120.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02923
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.2554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2900
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3250.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0151.5603
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7882956
X-RAY DIFFRACTIONr_scbond_it2.56331016
X-RAY DIFFRACTIONr_scangle_it3.8534.51002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.561 32 -
Rwork0.328 673 -
obs--92.16 %

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