1SVM: Large T antigen

Co-crystal structure of SV40 large T antigen helicase domain and ATP. Determined by X-ray diffraction at 1.94 Å resolution. Released 19 Oct 2004.

Method: X-ray diffraction
Resolution: 1.94 Å
Organism: Simian virus 40
Chains: 6
Atoms: 18,609
Mol. weight: 264.83 kDa
Ligands: ATP, MG, ZN
Released: 19 Oct 2004

Explore 1SVM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SVM contains 144 α-helices and 44 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: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-279	10
α-helix	285-293	9
α-helix	294-296	3
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-394	11
α-helix	401-414	14
β-strand	421-425	5	1
α-helix	432-443	12
β-strand	446-448	3	1
α-helix	457-461	5
α-helix	462-464	3
β-strand	470-472	3	1
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-509	3	2
β-strand	517-519	3	2
α-helix	520-522	3
β-strand	524-528	5	1
α-helix	535-538	4
β-strand	541-546	6	1
α-helix	551-558	8
α-helix	562-565	4
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-592	3
α-helix	593-606	14
α-helix	609-621	13

Chain B: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-293	9
α-helix	294-296	3
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-394	11
α-helix	401-414	14
β-strand	421-425	5	3
α-helix	432-443	12
β-strand	446-448	3	3
α-helix	454-456	3
α-helix	457-461	5
α-helix	462-464	3
β-strand	470-472	3	3
α-helix	481-483	3
α-helix	485-487	3
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-510	4	4
β-strand	516-519	4	4
α-helix	520-522	3
β-strand	524-528	5	3
α-helix	535-538	4
β-strand	541-546	6	3
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 C: 25 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-279	10
α-helix	285-294	10
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-327	11
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	5
α-helix	432-443	12
β-strand	445-448	4	5
α-helix	454-456	3
α-helix	457-461	5
α-helix	462-464	3
β-strand	469-472	4	5
α-helix	485-487	3
α-helix	490-494	5
α-helix	498-502	5
β-strand	507-510	4	6
β-strand	515-519	5	6
α-helix	520-522	3
β-strand	524-528	5	5
α-helix	535-538	4
β-strand	541-546	6	5
α-helix	551-558	8
α-helix	562-565	4
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-592	3
α-helix	593-606	14
α-helix	609-621	13

Chain D: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-279	10
α-helix	285-293	9
α-helix	294-296	3
α-helix	303-306	4
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	7
α-helix	432-443	12
β-strand	446-448	3	7
α-helix	457-462	6
β-strand	470-472	3	7
α-helix	481-483	3
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-510	4	8
β-strand	515-519	5	8
α-helix	520-522	3
β-strand	524-528	5	7
α-helix	535-538	4
β-strand	541-546	6	7
α-helix	551-558	8
α-helix	562-565	4
α-helix	572-582	11
α-helix	585-587	3
α-helix	590-604	15
α-helix	609-621	13

Chain E: 23 helices, 9 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	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-394	11
α-helix	401-414	14
β-strand	416	1	9
β-strand	419	1	9
β-strand	421-425	5	10
α-helix	432-443	12
β-strand	445-448	4	10
α-helix	457-461	5
α-helix	462-464	3
β-strand	469-472	4	10
α-helix	481-483	3
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-510	4	11
β-strand	516-519	4	11
α-helix	520-522	3
β-strand	524-528	5	10
α-helix	535-538	4
β-strand	541-546	6	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	609-621	13

Chain F: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-279	10
α-helix	285-293	9
α-helix	294-296	3
α-helix	303-306	4
α-helix	311-314	4
α-helix	317-327	11
α-helix	333-354	22
α-helix	357-375	19
α-helix	384-394	11
α-helix	401-414	14
β-strand	421-425	5	12
α-helix	432-443	12
β-strand	446-448	3	12
α-helix	457-462	6
β-strand	470-472	3	12
α-helix	481-483	3
α-helix	490-495	6
α-helix	498-502	5
β-strand	507-509	3	13
β-strand	517-519	3	13
α-helix	520-522	3
β-strand	524-528	5	12
α-helix	535-538	4
β-strand	541-546	6	12
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	609-621	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
large T antigen	A, B, C, D, E, F	protein	377	Simian virus 40	P03070 (AlphaFold model)

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

>1SVM_1 large T antigen (chains A, B, C, D, E, F)
GLKEHDFNPEEAEETKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQ
PSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLD
RMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDS
GKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQG
INNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPK
DYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLS
VYQKMKFNVAMGIGVLD

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	6
MG	Magnesium ion	Mg	6
ZN	Zinc ion	Zn	6

Primary citation

Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Gai, D., Zhao, R., Li, D. et al. Cell (2004) 119:47-60. DOI 10.1016/j.cell.2004.09.017 · 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
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
1Q1T 2.5 Å, Mouse Importin alpha: non-phosphorylated SV40 CN peptide complex

Browse structure collections

About this viewer

MolViewer shows 1SVM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.