2ITL: Large T antigen

The origin binding domain of the SV40 large T antigen bound to the functional pen palindrome DNA (23 bp). Determined by X-ray diffraction at 1.65 Å resolution. Released 12 Dec 2006.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Simian virus 40
Chains: 4
Atoms: 3,207
Mol. weight: 45.52 kDa
Released: 12 Dec 2006

Explore 2ITL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ITL contains 7 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	140-145	6
β-strand	146	1	1
β-strand	155-163	9	2
α-helix	165-178	14
β-strand	183-189	7	2
β-strand	192-204	13	2
α-helix	205-214	10
β-strand	221-225	5	2
β-strand	226	1	1
α-helix	229-237	9
β-strand	242-246	5	2

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	146	1	3
β-strand	156-163	8	4
α-helix	165-178	14
β-strand	183-189	7	4
β-strand	192-203	12	4
α-helix	205-213	9
β-strand	221-225	5	4
β-strand	226	1	3
α-helix	229-235	7
β-strand	242-246	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
24-nt PEN element of the SV40 DNA origin	W	DNA	24
24-nt PEN element of the SV40 DNA origin	C	DNA	24
large T antigen	A, B	protein	133	Simian virus 40	P03070 (AlphaFold model)

Sequence of entity 1 (W), FASTA

>2ITL_1 24-nt PEN element of the SV40 DNA origin (chains W)
AGAGGCCGAGGCGGCCTCGGCCTC

Sequence of entity 2 (C), FASTA

>2ITL_2 24-nt PEN element of the SV40 DNA origin (chains C)
AGAGGCCGAGGCCGCCTCGGCCTC

Sequence of entity 3 (A, B), FASTA

>2ITL_3 large T antigen (chains A, B)
GSHMKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISR
HNSYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEE
SLPGGLKEHDFNP

Primary citation

Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA. Bochkareva, E., Martynowski, D., Seitova, A. et al. EMBO J (2006) 25:5961-5969. DOI 10.1038/sj.emboj.7601452 · 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…
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
1Q1T 2.5 Å, Mouse Importin alpha: non-phosphorylated SV40 CN peptide complex

Browse structure collections

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