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- PDB-4fb3: Polyomavirus T-ag binds symmetrical repeats at the viral origin i... -

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Basic information

Entry
Database: PDB / ID: 4fb3
TitlePolyomavirus T-ag binds symmetrical repeats at the viral origin in an asymmetrical manner
Components
  • Large T antigen
  • ORI DNA oligonucleotide-Crick strand
  • ORI DNA oligonucleotide-Watson strand
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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA replication / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP binding / metal ion binding
Similarity search - Function
Replication Protein E1; Chain: A, - #20 / 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 ...Replication Protein E1; Chain: A, - #20 / 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 / 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 speciesMouse polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsBohm, A. / Harrison, C.J. / Schaffhausen, B.S. / Jiang, T.
CitationJournal: J.Virol. / Year: 2013
Title: Polyomavirus large T antigen binds symmetrical repeats at the viral origin in an asymmetrical manner.
Authors: Harrison, C. / Jiang, T. / Banerjee, P. / Meinke, G. / D'Abramo, C.M. / Schaffhausen, B. / Bohm, A.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ORI DNA oligonucleotide-Crick strand
W: ORI DNA oligonucleotide-Watson strand
A: Large T antigen
B: Large T antigen
E: Large T antigen


Theoretical massNumber of molelcules
Total (without water)66,8575
Polymers66,8575
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-62 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.150, 167.922, 77.728
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: DNA chain ORI DNA oligonucleotide-Crick strand


Mass: 7992.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#2: DNA chain ORI DNA oligonucleotide-Watson strand


Mass: 7992.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#3: Protein Large T antigen / LT / LT-AG


Mass: 16957.445 Da / Num. of mol.: 3 / Fragment: origin binding domain, UNP residues 290-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mouse polyomavirus / Gene: Large T-antigen / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P03074, UniProt: P0DOJ4*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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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: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 14% PEG 3350, 140 mM sodium citrate, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.79→117.46 Å / Num. all: 11102 / Num. obs: 11084 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.79→46.931 Å / SU ML: 0.89 / σ(F): 0 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 529 4.77 %random
Rwork0.2218 ---
obs0.2229 11080 99.89 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.572 Å2 / ksol: 0.285 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-23.8896 Å2-0 Å2-0 Å2
2---7.1107 Å20 Å2
3----16.7789 Å2
Refinement stepCycle: LAST / Resolution: 3.79→46.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 1060 0 0 3787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053993
X-RAY DIFFRACTIONf_angle_d1.0355612
X-RAY DIFFRACTIONf_dihedral_angle_d21.7591546
X-RAY DIFFRACTIONf_chiral_restr0.061624
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-4.17120.31361200.2812579X-RAY DIFFRACTION100
4.1712-4.77430.22321220.20812615X-RAY DIFFRACTION100
4.7743-6.01310.23651390.19842624X-RAY DIFFRACTION100
6.0131-46.93440.23571480.222733X-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)
16.4070.6778-1.32882.54010.22243.88430.2055-0.22630.02820.4055-0.1667-0.40060.07380.5090.00010.70660.0967-0.01790.6865-0.04040.7055-12.9371114.601-9.6727
24.8366-0.50660.58973.4522-0.26712.2714-0.0672-0.03460.0829-0.57130.1503-0.32810.08910.10090.00020.7638-0.04180.03130.6417-0.04540.69-15.995977.4075-18.1851
34.2269-1.5849-1.96744.56260.11627.2176-0.13860.0524-0.2659-0.38530.08150.2084-0.0843-0.33580.00030.70450.1762-0.05260.6704-0.0020.742-52.737138.01490.7183
40.6526-0.65920.2451.30041.90631.24890.25390.3315-0.10430.3556-0.26660.62360.0404-0.2963-0.00020.83360.15040.07741.08640.00551.0285-36.1699108.9848-15.0995
51.4689-0.9128-0.61730.09730.50831.04870.23790.2808-0.1298-0.0689-0.4559-0.0492-0.233-0.3874-0.00030.99410.08540.02831.0808-0.12280.8857-37.2462112.2153-14.0229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)
3X-RAY DIFFRACTION3(chain E)
4X-RAY DIFFRACTION4(chain C)
5X-RAY DIFFRACTION5(chain W)

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