9F3T: Large T antigen

Active SV40 LTAg complex with DNA (3D variability component_000, frame_010). Determined by electron microscopy at 3.0 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Betapolyomavirus macacae, synthetic construct
Chains: 7
Atoms: 17,938
Mol. weight: 256.31 kDa
Ligands: ATP
Released: 5 Feb 2025

Explore 9F3T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F3T contains 149 α-helices and 46 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-294	10
α-helix	299-301	3
α-helix	303-307	5
α-helix	311-314	4
α-helix	317-329	13
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	421-425	5	1
α-helix	432-443	12
β-strand	446-448	3	1
α-helix	454-460	7
α-helix	461-464	4
β-strand	470-472	3	1
β-strand	478	1	2
α-helix	480-483	4
α-helix	489-496	8
α-helix	498-502	5
β-strand	507-509	3	3
β-strand	517-519	3	3
α-helix	520-523	4
β-strand	524-527	4	1
β-strand	532	1	2
α-helix	535-538	4
β-strand	541-546	6	1
α-helix	551-557	7
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-582	11
α-helix	585-587	3
α-helix	593-604	12
α-helix	609-621	13

Chain B: 25 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-294	10
α-helix	299-301	3
α-helix	303-307	5
α-helix	311-314	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-397	14
α-helix	401-414	14
β-strand	421-425	5	4
α-helix	432-443	12
β-strand	446-448	3	4
α-helix	457-461	5
α-helix	462-464	3
β-strand	470-472	3	4
α-helix	480-483	4
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-511	5	5
β-strand	514-519	6	5
α-helix	520-522	3
β-strand	524-528	5	4
α-helix	535-538	4
β-strand	541-546	6	4
α-helix	551-559	9
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-606	17
α-helix	609-621	13

Chain C: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-294	10
α-helix	299-301	3
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-329	13
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-397	14
α-helix	401-414	14
β-strand	421-425	5	6
α-helix	432-443	12
β-strand	445-448	4	6
α-helix	456-460	5
α-helix	461-464	4
β-strand	469-475	7	6
α-helix	480-483	4
α-helix	485-487	3
α-helix	490-496	7
α-helix	498-502	5
β-strand	507-511	5	7
β-strand	514-519	6	7
α-helix	520-523	4
β-strand	524-528	5	6
α-helix	535-538	4
β-strand	541-546	6	6
α-helix	551-558	8
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-606	17
α-helix	609-621	13

Chain D: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-294	10
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-329	13
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-397	14
α-helix	401-414	14
β-strand	421-425	5	8
α-helix	432-443	12
β-strand	445-448	4	8
α-helix	457-462	6
β-strand	469-472	4	8
α-helix	480-483	4
α-helix	485-487	3
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-511	5	9
β-strand	514-519	6	9
α-helix	520-523	4
β-strand	524-528	5	8
α-helix	535-538	4
β-strand	543-546	4	8
α-helix	551-559	9
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-606	17
α-helix	609-621	13

Chain E: 25 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-279	10
α-helix	285-294	10
α-helix	299-301	3
α-helix	303-307	5
α-helix	311-314	4
α-helix	317-329	13
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-395	12
α-helix	401-414	14
β-strand	421-425	5	10
α-helix	432-443	12
β-strand	446-448	3	10
α-helix	457-461	5
α-helix	462-464	3
β-strand	470-472	3	10
α-helix	480-483	4
α-helix	485-487	3
α-helix	490-496	7
α-helix	498-502	5
β-strand	507-511	5	11
β-strand	514-519	6	11
α-helix	520-523	4
β-strand	524-528	5	10
α-helix	535-538	4
β-strand	543-546	4	10
α-helix	551-558	8
α-helix	562-565	4
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-606	17
α-helix	609-620	12

Chain F: 24 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-294	10
α-helix	299-301	3
α-helix	303-307	5
α-helix	311-314	4
α-helix	317-329	13
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-396	13
α-helix	401-414	14
β-strand	421-425	5	12
α-helix	432-441	10
β-strand	446-448	3	12
α-helix	454-462	9
β-strand	470-472	3	12
β-strand	477	1	13
α-helix	481-483	3
β-strand	488	1	13
α-helix	490-496	7
α-helix	498-502	5
β-strand	506-509	4	14
β-strand	517-520	4	14
α-helix	521-523	3
β-strand	524-527	4	12
α-helix	535-539	5
β-strand	543-546	4	12
α-helix	551-558	8
α-helix	562-565	4
α-helix	568-570	3
α-helix	572-582	11
α-helix	585-587	3
α-helix	593-606	14
α-helix	609-620	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large T antigen	A, B, C, D, E, F	protein	362	Betapolyomavirus macacae	P03070 (AlphaFold model)
DNA	S	DNA	8	synthetic construct

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9F3T_1 Large T antigen (chains A, B, C, D, E, F)
KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAA
IFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIE
EWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGG
KALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSV
KVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLE
KRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGV
LD

Sequence of entity 2 (S), FASTA

>9F3T_2 DNA (chains S)
TTTTTTTT

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6

Primary citation

Structural dynamics of DNA unwinding by a replicative helicase. Shahid, T., Danazumi, A.U., Tehseen, M. et al. Nature (2025) 641:240-249. DOI 10.1038/s41586-025-08766-w · PubMed

Other PDB entries of the same protein (UniProt P03070 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FUF 1.45 Å, Crystal structure of the SV40 large T antigen origin-binding domain
2IPR 1.5 Å, Origin binding domain of the SV40 large T antigen (residues 131-259). P21 crystal form
3QK2 1.64 Å, Structure-Based Analysis of the Interaction between the Simian Virus 40 T-Antigen Origin…
2ITL 1.65 Å, The origin binding domain of the SV40 large T antigen bound to the functional pen…
3QN2 1.66 Å, Structure-based design of a disulfide-linked oligomeric form of the Simian Virus 40…
5D9I 1.7 Å, SV40 Large T antigen origin binding domain bound to artificial DNA fork
4RXH 1.76 Å, Crystal Structure of Importin-alpha from Neurospora crassa complexed with SV40NLS
1SVM 1.94 Å, Co-crystal structure of SV40 large T antigen helicase domain and ATP
1SVL 1.95 Å, Co-crystal structure of SV40 large T antigen helicase domain and ADP
1Q1S 2.3 Å, Mouse Importin alpha- phosphorylated SV40 CN peptide complex
2NL8 2.3 Å, The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp…
2NTC 2.4 Å, Crystal Structure of sv40 large T antigen origin binding domain with DNA

Browse structure collections

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