9kak

CryoEM structure of LTag bound to SV40 AT half origin DNA

Method: ELECTRON MICROSCOPY D_max: 127.2 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Large T antigen

Betapolyomavirus macacae

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–DNA Homooligomer Protein × 6 DNA 2 PDB declaration: octameric（8） Consistent with all polymer counts	Chain A； UniProt 266–627 Chain B； UniProt 266–627 Chain C； UniProt 266–627 Chain D； UniProt 266–627 Chain E； UniProt 266–627 Chain F； UniProt 266–627	Not recorded	DNA × 1 DNA × 1 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

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 9KAK	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 method 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 method 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 oligomeric state 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 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 method 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 method 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
1SVL Co-crystal structure of SV40 large T antigen helicase domain and ADP Deposited 2004-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein 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	Not recorded	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
1SVM Co-crystal structure of SV40 large T antigen helicase domain and ATP Deposited 2004-03-29	Different construct Different oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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：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 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：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 method 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 method 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 method 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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	Parsed fields agree	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	LT_SV40
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–362； UniProt 266–627 Author chain B； PDBConstruct 1–362； UniProt 266–627 Author chain C； PDBConstruct 1–362； UniProt 266–627 Author chain D； PDBConstruct 1–362； UniProt 266–627 Author chain E； PDBConstruct 1–362； UniProt 266–627 Author chain F； PDBConstruct 1–362； UniProt 266–627

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9kak
Deposition date deposition_date	2024-10-29
Structure title title	CryoEM structure of LTag bound to SV40 AT half origin DNA
Keywords keywords	Helicase, ATPase, AT half origin, AMP-PNP, DNA replication, TRANSLOCASE; TRANSLOCASE
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	40.38 Å
Radius of gyration Rg (electron density) rg_electron	40.11 Å
Forward intensity I(0) i0	998936000.00
Molecular weight molecular_weight	261370.0 kDa
Excluded volume excluded_volume	327720 Å³
Envelope volume envelope_volume	429880 Å³
Hydration-shell volume shell_volume	84282 Å³
Envelope diameter envelope_diameter	131.6 Å
Shell Rg shell_rg	49.26 Å
Envelope Rg envelope_rg	39.55 Å
Shape Rg shape_rg	40.12 Å
Total Rg total_rg	40.52 Å
Total atoms total_atoms	36569
Residues n_residues	2197
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	127.2 Å
Rg (real space) rg_real	40.18 Å
Rg uncertainty (real space) rg_real_error	0.97 Å
I(0) (real space) i0_real	9.9890e+08
I(0) uncertainty (real space) i0_real_error	1.8290e+07
Rg (reciprocal space) rg_reciprocal	40.38 Å
I(0) (reciprocal space) i0_reciprocal	999100000.0000
Solution quality estimate total_estimate	0.8901
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.2 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	188900000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.939

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Large T antigen
Molecular weight formula_weight	41812.7 kDa
EC 编号 ec_number	5.6.2.4
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	36569

KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD

来源 Source

来源生物 organism	Betapolyomavirus macacae
NCBI Class编号 ncbi_taxonomy_id	1891767
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	DNA
Molecular weight formula_weight	3087.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

AAAAAAAAAA

Entity 3 Entity 3 polymer

Description description	DNA
Molecular weight formula_weight	4517.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TTTTTTTTTTTTTTT

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	198000

fit	/app/data/saxs_computation/ka/9kak/9kak.fit
pddf	/app/data/pr_computation/ka/9kak/9kak.pr.out
profile	/app/data/saxs_computation/ka/9kak/9kak.dat

CryoEM structure of LTag bound to SV40 AT half origin DNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

Large T antigen

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)