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- PDB-3qn2: Structure-based design of a disulfide-linked oligomeric form of t... -

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Basic information

Entry
Database: PDB / ID: 3qn2
TitleStructure-based design of a disulfide-linked oligomeric form of the Simian Virus 40 (SV40) large T antigen DNA binding domain
ComponentsLarge T antigenLarge tumor antigen
KeywordsHYDROLASE / 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 / 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 / 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
CITRATE ANION / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.661 Å
AuthorsMeinke, G. / Bullock, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain.
Authors: Meinke, G. / Phelan, P. / Fradet-Turcotte, A. / Archambault, J. / Bullock, P.A.
History
DepositionFeb 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5162
Polymers15,3271
Non-polymers1891
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.933, 83.933, 35.872
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 15326.590 Da / Num. of mol.: 1 / Fragment: origin binding domain / Mutation: F151C, C216A, D256C
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-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 17286 / Num. obs: 17264 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 44.8
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 20.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 7.1 / Num. unique all: 1732 / Rsym value: 0.5 / % possible all: 99.5

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Processing

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

2fuf


Resolution: 1.661→41.967 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 875 5.07 %RANDOM
Rwork0.1696 ---
obs0.1706 16962 99.91 %-
all-17286 --
Solvent computationShrinkage radii: 1.25 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.894 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7718 Å2-0 Å20 Å2
2---1.7718 Å20 Å2
3---3.5435 Å2
Refinement stepCycle: LAST / Resolution: 1.661→41.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 13 127 1136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051081
X-RAY DIFFRACTIONf_angle_d0.921471
X-RAY DIFFRACTIONf_dihedral_angle_d11.18388
X-RAY DIFFRACTIONf_chiral_restr0.073166
X-RAY DIFFRACTIONf_plane_restr0.004186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.661-1.76480.26711530.23542698X-RAY DIFFRACTION100
1.7648-1.90110.21461640.17242704X-RAY DIFFRACTION100
1.9011-2.09240.1811360.15032706X-RAY DIFFRACTION100
2.0924-2.39510.17471510.16162733X-RAY DIFFRACTION100
2.3951-3.01750.18791470.17272719X-RAY DIFFRACTION100
3.0175-41.97990.18751240.16762829X-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)
10.99490.12550.02881.1023-0.1960.64330.0722-0.0618-0.03040.102-0.0181-0.1220.08670.0111-0.04750.1378-0.0149-0.00020.1056-0.010.118428.228746.55787.1604
22.9295-2.2745-1.46682.78412.35152.2875-0.0292-0.46440.32460.12390.2194-0.17420.25780.4236-0.1820.1172-0.00970.01610.214-0.03380.20736.375853.15894.2422
30.56520.58170.29411.15640.08830.58950.1267-0.0035-0.05710.1249-0.01910.06510.0054-0.0564-0.07440.1299-0.00940.00920.09860.00480.13622.659245.23136.4415
41.46551.0969-0.03921.6011-0.0140.73180.3299-0.11120.18920.0722-0.33620.55980.07420.0812-0.00250.529-0.183-0.15740.61430.07670.961913.181955.52953.7865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 131:200)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 201:216)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 217:248)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 249:257)

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