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- PDB-4gdf: A Crystal Structure of SV40 Large T Antigen -

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Basic information

Entry
Database: PDB / ID: 4gdf
TitleA Crystal Structure of SV40 Large T Antigen
Components
  • (DNA (32-MER)) x 2
  • Large T antigenLarge tumor antigen
KeywordsHYDROLASE/DNA / SV40 Large T Antigen / DNA replication / helicase / primase / HYDROLASE-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 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 / DNA replication / 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 / 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. ...Large T antigen, SV40, domain 3 / Zinc finger, large T-antigen D1 domain / 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 / 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
DNA / DNA (> 10) / Large T antigen / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChang, Y.P. / Xu, M. / Chen, X.S.
CitationJournal: Cell Rep / Year: 2013
Title: Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen.
Authors: Chang, Y.P. / Xu, M. / Machado, A.C. / Yu, X.J. / Rohs, R. / Chen, X.S.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
C: DNA (32-MER)
D: DNA (32-MER)
E: Large T antigen
F: Large T antigen
G: DNA (32-MER)
H: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,43312
Polymers269,1718
Non-polymers2624
Water1,42379
1
A: Large T antigen
B: Large T antigen
C: DNA (32-MER)
D: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7166
Polymers134,5864
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-54 kcal/mol
Surface area55920 Å2
MethodPISA
2
E: Large T antigen
F: Large T antigen
G: DNA (32-MER)
H: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7166
Polymers134,5864
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-54 kcal/mol
Surface area55990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.633, 128.307, 166.120
Angle α, β, γ (deg.)90.00, 89.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Large T antigen / Large tumor antigen


Mass: 57450.445 Da / Num. of mol.: 4 / Fragment: UNP residues 131-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DH70, UniProt: P03070*PLUS
#2: DNA chain DNA (32-MER)


Mass: 9891.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nucleic acid synthesis
#3: DNA chain DNA (32-MER)


Mass: 9793.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: nucleic acid synthesis
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 100 mM bis-Tris (pH 6.75), 20% (v/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9997 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 28, 2009
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 172018 / Num. obs: 70174 / % possible obs: 93.2 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 88.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2549 3317 random
Rwork0.2269 --
obs-65350 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16140 2612 4 79 18835

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