2NL8: Large T antigen

The origin binding domain of the SV40 large T antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3). Determined by X-ray diffraction at 2.3 Å resolution. Released 12 Dec 2006.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Simian virus 40
Chains: 2
Atoms: 1,406
Mol. weight: 20.84 kDa
Released: 12 Dec 2006

Explore 2NL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NL8 contains 3 α-helices and 7 β-strands across 1 chain. 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	146	1	1
β-strand	156-163	8	2
α-helix	165-178	14
β-strand	183-189	7	2
β-strand	192-203	12	2
α-helix	205-212	8
β-strand	221-225	5	2
β-strand	226	1	1
α-helix	229-238	10
β-strand	241-246	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
18-nt PEN element of the SV40 DNA origin	W	DNA	18
large T antigen	A	protein	133	Simian virus 40	P03070 (AlphaFold model)

Sequence of entity 1 (W), FASTA

>2NL8_1 18-nt PEN element of the SV40 DNA origin (chains W)
CGAGGCCATCATGGCCTC

Sequence of entity 2 (A), FASTA

>2NL8_2 large T antigen (chains A)
GSHMKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISR
HNSYNHNILFFLTPHRHRVSAINNYAQKLSTFSFLICKGVNKEYLMYSALTRDPFSVIEE
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…
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
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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