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- PDB-3qk2: Structure-Based Analysis of the Interaction between the Simian Vi... -

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Basic information

Entry
Database: PDB / ID: 3qk2
TitleStructure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA
ComponentsLarge T antigen
KeywordsDNA BINDING PROTEIN / origin binding domain / DNA replication
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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / 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 / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / 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
THIOCYANATE ION / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsMeinke, G. / Bullock, P.A. / Bohm, A.
CitationJournal: J.Virol. / Year: 2011
Title: Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA.
Authors: Meinke, G. / Phelan, P.J. / Fradet-Turcotte, A. / Bohm, A. / Archambault, J. / Bullock, P.A.
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5492
Polymers15,4911
Non-polymers581
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.969, 63.772, 62.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 15490.752 Da / Num. of mol.: 1 / Fragment: origin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Plasmid: pGEX-4T / 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: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion
Details: 0.2 M thiocyanate [SCN], 17.5% PEG 3350, 5% glycerol, VAPOR DIFFUSION, temperature 278K

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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: Jun 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 15789 / Num. obs: 15764 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 29.38
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 4.46 / Num. unique all: 14985 / Rsym value: 0.474 / % possible all: 90.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FUF

2fuf


Resolution: 1.643→44.807 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 786 4.99 %RANDOM
Rwork0.1642 ---
obs0.1654 15626 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.301 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8693 Å2-0 Å2-0 Å2
2---1.0029 Å2-0 Å2
3----4.8664 Å2
Refinement stepCycle: LAST / Resolution: 1.643→44.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 3 129 1197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071153
X-RAY DIFFRACTIONf_angle_d1.1121567
X-RAY DIFFRACTIONf_dihedral_angle_d13.033426
X-RAY DIFFRACTIONf_chiral_restr0.073171
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.643-1.7460.2711320.21932430X-RAY DIFFRACTION99
1.746-1.88080.23761240.17722484X-RAY DIFFRACTION100
1.8808-2.07010.18231310.15382459X-RAY DIFFRACTION100
2.0701-2.36960.19651460.15792475X-RAY DIFFRACTION100
2.3696-2.98540.19361170.17332528X-RAY DIFFRACTION100
2.9854-44.82370.1641360.15612602X-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)
10.3106-0.36360.36720.4763-0.48060.4830.10380.03890.0411-0.1643-0.02570.00490.0867-0.021-0.06330.20830.03070.00470.16720.01620.1628-18.2983-17.1817-12.0378
20.3728-0.4210.17330.4783-0.17170.9537-0.0512-0.0040.0154-0.01870.06450.0215-0.1015-0.1051-0.00940.14210.0052-0.00160.12230.00020.1287-17.3042-14.21622.517
30.0392-0.0508-0.09120.27360.22080.75880.0039-0.00070.0115-0.00370.0398-0.08670.0030.0919-0.04340.13760.0028-0.00990.135-0.0050.1523-10.7035-19.19730.6998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 129:148)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 149:211)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 212:261)

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