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1svl

Co-crystal structure of SV40 large T antigen helicase domain and ADP

Method: X-RAY DIFFRACTION Dmax: 112.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

large T antigen

Simian virus 40

UniProt P03070

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 251–627 Chain B； UniProt 251–627 Chain C； UniProt 251–627 Fragment：HELICASE DOMAIN ZN ZINC ION × 6 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；277 K；Tris, magnesium chloride, PEG 8000, DTT, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.95 Å R-free 0.264

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1SVL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EJL MOUSE IMPORTIN ALPHA-SV40 LARGE T ANTIGEN NLS PEPTIDE COMPLEX Deposited 2000-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 126–132（7 aa） Fragment：NLS (NUCLEAR LOCALIZATION SIGNAL) MONOPARTITE PEPTIDE, RESIDUES 126-132
Chain B 126–132（7 aa） Fragment：NLS (NUCLEAR LOCALIZATION SIGNAL) MONOPARTITE PEPTIDE, RESIDUES 126-132
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；sodium citrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.80 Å R-free 0.254
1GH6 RETINOBLASTOMA POCKET COMPLEXED WITH SV40 LARGE T ANTIGEN Deposited 2000-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 7–117（111 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 3.20 Å R-free 0.314
1N25 Crystal structure of the SV40 Large T antigen helicase domain Deposited 2002-10-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 260–627（368 aa） Fragment：helicase domain
Chain B 260–627（368 aa） Fragment：helicase domain
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；glycerol, DTT, Hepes, NaCl, EtOH, EDTA, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.276
1Q1S Mouse Importin alpha- phosphorylated SV40 CN peptide complex Deposited 2003-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 110–133（24 aa） Fragment：CN peptide - Ser112 chemically phosphorylated
Chain B 110–133（24 aa） Fragment：CN peptide - Ser112 chemically phosphorylated
Chain C 70–529（460 aa） Fragment：NLS binding domain (70-529)
Mutation：S120A, S123A, T124A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S120A, S123A, T124A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Citrate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.221
1Q1T Mouse Importin alpha: non-phosphorylated SV40 CN peptide complex Deposited 2003-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 110–133（24 aa） Fragment：CN peptide
Chain B 110–133（24 aa） Fragment：CN peptide
Chain C 70–529（460 aa） Fragment：NLS binding domain (70-529)
Mutation：S120A, S123A, T124A Mutation：S120A, S123A, T124A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；Sodium Citrate, DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.233
1SVM Co-crystal structure of SV40 large T antigen helicase domain and ATP Deposited 2004-03-29 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain B 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain C 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain D 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain E 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain F 251–627（377 aa） Fragment：HELICASE DOMAIN
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；277 K；Tris, magnesium chloride, PEG 8000, DTT, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.94 Å R-free 0.241
1SVO Structure of SV40 large T antigen helicase domain Deposited 2004-03-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 251–627（377 aa） Fragment：HELICASE DOMAIN
Chain B 251–627（377 aa） Fragment：HELICASE DOMAIN
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；HEPES, NACL, ETHANOL, EDTA, DTT, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.271
1TBD SOLUTION STRUCTURE OF THE ORIGIN DNA BINDING DOMAIN OF SV40 T-ANTIGEN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–260（130 aa） Fragment：DNA BINDING DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；303 K
Resolution not provided
1Z1D Structural Model for the interaction between RPA32 C-terminal domain and SV40 T antigen origin binding domain. Deposited 2005-03-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 131–259（129 aa） Fragment：SV40 T antigen Origin binding domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.03 M；Pressure ambient
NMR sample composition 0.2mM RPA32C U-15N, 0.6mM Tag-OBD, 20mM Tris buffer pH 7.0, 2 mM DTT, 5mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2mM Tag-OBD U-15N, 0.6mM RPA32C, 20mM Tris buffer pH 7.0, 2mM DTT, 5mM MgCl2, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2FUF Crystal structure of the SV40 large T antigen origin-binding domain Deposited 2006-01-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 131–260（130 aa） Fragment：DNA binding domain (residues 131-259)
Non-standard monomer：Yes (specific site not provided by mmCIF) FLC CITRATE ANION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；298 K；1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.45 Å R-free 0.189
2IF9 Crystal Structure of SV40 T-antigen origin binding domain disulfide-linked dimer Deposited 2006-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 131–260（130 aa） Fragment：origin binding domain
Chain B 131–260（130 aa） Fragment：origin binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；30 % peg 4000, 0.1M sodium citrate (pH 5.6), 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.59 Å R-free 0.296
2IPR Origin binding domain of the SV40 large T antigen (residues 131-259). P21 crystal form Deposited 2006-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Chain B 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；300 K；20 mM NaSCN, 10% P4K, 0.1 Tris, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Resolution 1.50 Å R-free 0.204
2ITJ Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form Deposited 2006-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Chain B 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；20 mM NaAc, 20% PEG4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 2.50 Å R-free 0.289
2ITL The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp) Deposited 2006-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric
Chain A 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Chain B 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；20 mM di-ammonium hydrogen citrate, 20% PEG 3000, and 10 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.65 Å R-free 0.251
2NL8 The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3) Deposited 2006-10-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 131–259（129 aa） Fragment：Origin binding domain (residues 131-259)
Mutation：CYS216SER No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；297 K；20 mM NaAcetate, 20% PEG 3000 + 4% PEG 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.30 Å R-free 0.299
2NTC Crystal Structure of sv40 large T antigen origin binding domain with DNA Deposited 2006-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 131–260（130 aa） Fragment：Origin binding domain (residues 131-259)
Chain B 131–260（130 aa） Fragment：Origin binding domain (residues 131-259)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；273 K；0.1 M sodium cacodylate pH 6.5, 0.1 M calcium acetate, 30 % v/v peg 8000, 20 % glycerol, VAPOR DIFFUSION, temperature 273K
Resolution 2.40 Å R-free 0.287
2TBD SV40 T ANTIGEN DNA-BINDING DOMAIN, NMR, 30 STRUCTURES Deposited 1997-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–260（130 aa） Fragment：DNA BINDING DOMAIN, RESIDUES 131 - 260
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；303 K
Resolution not provided
3QK2 Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin Binding Domain and Single-Stranded DNA Deposited 2011-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–260（130 aa） Fragment：origin binding domain
Non-standard monomer：Yes (specific site not provided by mmCIF) SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；278 K；0.2 M thiocyanate [SCN], 17.5% PEG 3350, 5% glycerol, VAPOR DIFFUSION, temperature 278K
Resolution 1.64 Å R-free 0.187
3QN2 Structure-based design of a disulfide-linked oligomeric form of the Simian Virus 40 (SV40) large T antigen DNA binding domain Deposited 2011-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–260（130 aa） Fragment：origin binding domain
Mutation：F151C, C216A, D256C FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.6 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.66 Å R-free 0.191
4FGN Crystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA Deposited 2012-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 131–260（130 aa） Fragment：origin binding domain, UNP residues 131-260
Chain B 131–260（130 aa） Fragment：origin binding domain, UNP residues 131-260
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.1M sodium acetate pH 4.6, .2M ammonium sulfate, 30 % Peg 4000, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.20 Å R-free 0.267
4RXH Crystal Structure of Importin-alpha from Neurospora crassa complexed with SV40NLS Deposited 2014-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 125–132（8 aa）
Chain C 125–132（8 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；297 K；20 Mm Bicine pH 8.5, 20%(w/v) PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Resolution 1.76 Å R-free 0.211
5D9I SV40 Large T antigen origin binding domain bound to artificial DNA fork Deposited 2015-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 131–260（130 aa） Fragment：unp residues 131-260
Chain B 131–260（130 aa） Fragment：unp residues 131-260
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；100 mM Tris, 300 mM NH4Cl, 28% polyethylene glycol [PEG] 4000, 20 mM CaCl2
Resolution 1.70 Å R-free 0.223
9EVH SV40 large T antigen assembly with DNA in presence of ADP Deposited 2024-03-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 1–708（708 aa）
Chain B 1–708（708 aa）
Chain C 1–708（708 aa）
Chain D 1–708（708 aa）
Chain E 1–708（708 aa）
Chain F 1–708（708 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；200 mM NaCl, 50 mM Tris-HCl (pH 8.0), 1 mM ADP.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
9EVP SV40 LTAg assembly with DNA in presence of AMPPNP and Mg2+. Deposited 2024-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM TrisHCl (pH 7.5), 1 mM DTT, 100 mM NaCl, 5 mM MgCl, 3 mM AMP-PMP.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9EXD SV40 LTAg assembly in presence of ATP. Deposited 2024-04-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–708（708 aa）
Chain B 1–708（708 aa）
Chain C 1–708（708 aa）
Chain D 1–708（708 aa）
Chain E 1–708（708 aa）
Chain F 1–708（708 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；200 mM NaCl, 50 mM Tris-HCl (pH 8.0), 1 mM ATP.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9F3T Active SV40 LTAg complex with DNA (3D variability component_000, frame_010). Deposited 2024-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F3U Active SV40 LTAg complex with DNA (3D variability component_001, frame_010). Deposited 2024-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F5I Active SV40 LTAg complex with DNA (3D variability component_000, frame_005). Deposited 2024-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F73 Active SV40 LTAg complex with DNA (3D variability component_002, frame_015). Deposited 2024-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F74 Active SV40 LTAg complex with DNA (3D variability component_000, frame_015). Deposited 2024-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F75 Active SV40 LTAg complex with DNA (3D variability component_000, frame_019). Deposited 2024-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F7N Active SV40 LTAg complex with DNA (3D variability component_000, frame_000). Deposited 2024-05-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F9N Active SV40 LTAg complex with DNA (3D variability component_001, frame_005). Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F9O Active SV40 LTAg complex with DNA (3D variability component_001, frame_015). Deposited 2024-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F9W Active SV40 LTAg complex with DNA (3D variability component_001, frame_019). Deposited 2024-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9F9X Active SV40 LTAg complex with DNA (3D variability component_001, frame_000). Deposited 2024-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9FA1 Active SV40 LTAg complex with DNA (3D variability component_002, frame_010). Deposited 2024-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9FA2 Active SV40 LTAg complex with DNA (3D variability component_002, frame_005). Deposited 2024-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9FB0 Active SV40 LTAg complex with DNA (3D variability component_002, frame_019). Deposited 2024-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9FB4 SV40 large T antigen assembly with DNA in presence of ATP. Deposited 2024-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；200 mM NaCl, 50 mM Tris-HCl (pH 8.0), 1 mM ATP.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9FB5 Active SV40 LTAg complex with DNA (3D variability component_002, frame_000). Deposited 2024-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50 mM HEPES (pH 7.5), 1 mM ATP, 3 mM MgCl2, 1 mM DTT and 50 mM NaCl.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9FB6 SV40 large T antigen assembly with DNA in presence of ATP. Deposited 2024-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；200 mM NaCl, 50 mM Tris-HCl (pH 8.0), 1 mM ATP.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9KAE CryoEM structure of LTag bound to SV40 EP half origin DNA Deposited 2024-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9KAK CryoEM structure of LTag bound to SV40 AT half origin DNA Deposited 2024-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: octameric
Chain A 266–627（362 aa）
Chain B 266–627（362 aa）
Chain C 266–627（362 aa）
Chain D 266–627（362 aa）
Chain E 266–627（362 aa）
Chain F 266–627（362 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

44 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TALA_SV40
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–377； UniProt 251–627 Author chain B； PDBConstruct 1–377； UniProt 251–627 Author chain C； PDBConstruct 1–377； UniProt 251–627

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1svl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1svl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1svl
Deposition date deposition_date2004-03-29
Structure title titleCo-crystal structure of SV40 large T antigen helicase domain and ADP
Keywords keywordsAAA+ fold, Viral protein; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.75 Å
Radius of gyration Rg (electron density) rg_electron34.23 Å
Forward intensity I(0) i0237829000.00
Molecular weight molecular_weight126880.0 kDa
Excluded volume excluded_volume160110 ų
Envelope volume envelope_volume205090 ų
Hydration-shell volume shell_volume50168 ų
Envelope diameter envelope_diameter117.7 Å
Shell Rg shell_rg40.78 Å
Envelope Rg envelope_rg33.72 Å
Shape Rg shape_rg34.23 Å
Total Rg total_rg34.73 Å
Total atoms total_atoms8889
Residues n_residues1087
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.9 Å
Rg (real space) rg_real34.71 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real2.3780e+08
I(0) uncertainty (real space) i0_real_error3.8620e+06
Rg (reciprocal space) rg_reciprocal34.74 Å
I(0) (reciprocal space) i0_reciprocal237800000.0000
Solution quality estimate total_estimate0.6633
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.7 Å
Skewness Skewness skewness0.320
Kurtosis Kurtosis kurtosis-0.290
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha30130000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.997; Smooth: 0.843
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1svla_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1svlb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain
Domain ID domain_idd1svlc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (9 domains)

Domain ID domain_id1svlA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily510 — Zinc finger, large T-antigen D1 domain
Domain ID domain_id1svlA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily70 — Large T antigen, SV40, domain 3
Domain ID domain_id1svlA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1svlB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily510 — Zinc finger, large T-antigen D1 domain
Domain ID domain_id1svlB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily70 — Large T antigen, SV40, domain 3
Domain ID domain_id1svlB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1svlC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily510 — Zinc finger, large T-antigen D1 domain
Domain ID domain_id1svlC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily70 — Large T antigen, SV40, domain 3
Domain ID domain_id1svlC03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)