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- PDB-1n25: Crystal structure of the SV40 Large T antigen helicase domain -

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Basic information

Entry
Database: PDB / ID: 1n25
TitleCrystal structure of the SV40 Large T antigen helicase domain
ComponentsLarge T AntigenLarge tumor antigen
KeywordsVIRAL PROTEIN / Helicase domain
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
Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / 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 ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / Large T antigen, polyomaviridae / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsLi, D. / Zhao, R. / Lilyestrom, W. / Gai, D. / Zhang, R. / DeCaprio, J.A. / Fanning, E. / Jochimiak, A. / Szakonyi, G. / Chen, X.S.
CitationJournal: Nature / Year: 2003
Title: Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen
Authors: Li, D. / Zhao, R. / Lilyestrom, W. / Gai, D. / Zhang, R. / DeCaprio, J.A. / Fanning, E. / Jochimiak, A. / Szakonyi, G. / Chen, X.S.
History
DepositionOct 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Large T Antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1334
Polymers85,0032
Non-polymers1312
Water0
1
A: Large T Antigen
B: Large T Antigen
hetero molecules

A: Large T Antigen
B: Large T Antigen
hetero molecules

A: Large T Antigen
B: Large T Antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,40012
Polymers255,0086
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)120.321, 120.321, 132.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Large T Antigen / Large tumor antigen


Mass: 42501.301 Da / Num. of mol.: 2 / Fragment: helicase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P03070
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: glycerol, DTT, Hepes, NaCl, EtOH, EDTA, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
3250 mM1dropNaCl
41 mMEDTA1drop
510 mMdithiothreitol1drop
620 mMdithiothreitol1reservoir
750 mMHEPES1reservoirpH7.6
8105 mM1reservoirNaCl
95 %ethanol1reservoir
101 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.074385 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jun 20, 2001 / Details: undulator A
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074385 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 28059 / Num. obs: 27610 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 16.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2776 / Rsym value: 0.544 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 171257

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Processing

Software
NameVersionClassification
HKL-2000data collection
TRUNCATEdata reduction
SOLVEphasing
CNSrefinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1333 5 %random
Rwork0.243 ---
all-27715 --
obs-26688 96.3 %-
Solvent computationSolvent model: anisotropic / Bsol: 30.79 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 30.79 Å2
Baniso -1Baniso -2Baniso -3
1-13.866 Å23.912 Å20 Å2
2--13.866 Å20 Å2
3----27.732 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4675 Å0.3974 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6238 Å0.573 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 0 0 5806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.374
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_improper_angle_d0.799
X-RAY DIFFRACTIONc_dihedral_angle_d21.54
X-RAY DIFFRACTIONc_mcbond_it2.953
X-RAY DIFFRACTIONc_mcangle_it4.57
X-RAY DIFFRACTIONc_scbond_it4.926
X-RAY DIFFRACTIONc_scangle_it7.546
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.392 49 5 %
Rwork0.367 921 -
obs-970 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
Refinement
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.379
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.54
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.799

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