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- PDB-2ntc: Crystal Structure of sv40 large T antigen origin binding domain w... -

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Basic information

Entry
Database: PDB / ID: 2ntc
TitleCrystal Structure of sv40 large T antigen origin binding domain with DNA
Components
  • (21-nt PEN element of the SV40 DNA origin) x 2
  • large T antigen
KeywordsDNA binding protein/DNA / origin binding domain / protein-DNA complex / replication / 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 / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / isomerase activity / helicase activity / single-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 / DNA unwinding involved in DNA replication / 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 / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / ATP hydrolysis activity / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBohm, A. / Meinke, G. / Bullock, P.A.
CitationJournal: Plos Biol. / Year: 2007
Title: The Crystal Structure of the SV40 T-Antigen Origin Binding Domain in Complex with DNA
Authors: Meinke, G. / Phelan, P. / Moine, S. / Bochkareva, E. / Bochkarev, A. / Bullock, P.A. / Bohm, A.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 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: 21-nt PEN element of the SV40 DNA origin
C: 21-nt PEN element of the SV40 DNA origin
A: large T antigen
B: large T antigen


Theoretical massNumber of molelcules
Total (without water)43,7184
Polymers43,7184
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.489, 68.341, 97.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe asymmetric unit contains two t-antigen origin binding domain molecules bound to a dna target that contains two high affinity binding sites

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Components

#1: DNA chain 21-nt PEN element of the SV40 DNA origin


Mass: 6415.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 21-nt PEN element of the SV40 DNA origin


Mass: 6473.186 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein large T antigen


Mass: 15414.633 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: pGEX-1lT / 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.: 77 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 273 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.1 M calcium acetate, 30 % v/v peg 8000, 20 % glycerol, VAPOR DIFFUSION, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2calcium acetate11
3peg 800011
4glycerol11
5sodium cacodylate12
6calcium acetate12
7peg 800012
8glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2005 / Details: crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 15755 / Num. obs: 15314 / % possible obs: 90.1 % / Observed criterion σ(I): 2.1 / Redundancy: 12.2 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 2.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: t antigen origin binding domain and four base pairs duplex dna

Resolution: 2.4→38.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.329 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.523 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28692 772 4.9 %RANDOM
Rwork0.2049 ---
all0.2088 15755 --
obs0.2088 14921 90.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---4.37 Å20 Å2
3---5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 855 0 77 2995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213079
X-RAY DIFFRACTIONr_angle_refined_deg2.0132.2994343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0125251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09923.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6211510
X-RAY DIFFRACTIONr_chiral_restr0.1080.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022041
X-RAY DIFFRACTIONr_nbd_refined0.2390.21239
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4590.23
X-RAY DIFFRACTIONr_mcbond_it0.8781.51299
X-RAY DIFFRACTIONr_mcangle_it1.57522055
X-RAY DIFFRACTIONr_scbond_it1.86832295
X-RAY DIFFRACTIONr_scangle_it2.8664.52288
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 29 -
Rwork0.297 706 -
obs--58.33 %
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)
18.39833.35125.67219.91593.59619.7363-0.088-0.265-0.933-0.15930.67710.94471.0058-0.1001-0.5891-0.2066-0.05080.03150.05030.07740.2779-9.261-29.1451.976
26.867-4.03742.28047.24871.30112.1889-0.2292-0.52191.07030.7454-0.3025-1.2936-0.93270.13390.5317-0.08750.0462-0.14490.0495-0.0010.543722.96525.5329.598
31.1212-0.86820.02610.3252-0.09370.33350.09390.0082-0.1424-0.8168-0.1762-0.0307-0.00250.00340.0823-0.0638-0.00260.0385-0.2667-0.03880.112411.791-2.972-17.801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC233 - 258105 - 130
2X-RAY DIFFRACTION2BD233 - 258105 - 130
3X-RAY DIFFRACTION3WA2 - 212 - 21
4X-RAY DIFFRACTION3CB23 - 431 - 21

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