1N25: SV40 Large T antigen helicase domain

Crystal structure of the SV40 Large T antigen helicase domain. Determined by X-ray diffraction at 2.8 Å resolution. Released 3 Jun 2003.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Simian virus 40
Chains: 2
Atoms: 5,868
Mol. weight: 85.13 kDa
Ligands: ZN
Released: 3 Jun 2003

Explore 1N25 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N25 contains 47 α-helices and 14 β-strands across 2 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: 23 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-280	11
α-helix	285-292	8
α-helix	293-296	4
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	445-448	4	1
α-helix	457-461	5
α-helix	462-464	3
β-strand	469-475	7	1
α-helix	490-494	5
α-helix	498-502	5
β-strand	507-511	5	2
β-strand	514-519	6	2
α-helix	520-523	4
β-strand	524-528	5	1
α-helix	535-538	4
β-strand	543-546	4	1
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	609-620	12

Chain B: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	270-278	9
α-helix	285-292	8
α-helix	293-296	4
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	3
α-helix	432-443	12
β-strand	446-448	3	3
α-helix	457-461	5
α-helix	462-464	3
β-strand	470-475	6	3
α-helix	490-494	5
α-helix	495-497	3
α-helix	498-501	4
β-strand	507-511	5	4
β-strand	514-519	6	4
α-helix	520-523	4
β-strand	524-528	5	3
α-helix	535-538	4
β-strand	543-546	4	3
α-helix	551-559	9
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	protein	368	Simian virus 40	P03070 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1N25_1 Large T Antigen (chains A, B)
EEAEETKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEK
HYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGST
GSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAAL
LELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRD
YLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLER
SEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNV
AMGIGVLD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen. Li, D., Zhao, R., Lilyestrom, W. et al. Nature (2003) 423:512-518. DOI 10.1038/nature01691 · 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

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