5D9I: SV40 Large T antigen origin binding domain

SV40 Large T antigen origin binding domain bound to artificial DNA fork. Determined by X-ray diffraction at 1.7 Å resolution. Released 9 Sept 2015.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Simian virus 40, synthetic construct
Chains: 4
Atoms: 3,376
Mol. weight: 44.76 kDa
Ligands: CA
Released: 9 Sept 2015

Explore 5D9I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D9I contains 13 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	130-133	4
α-helix	140-145	6
β-strand	146	1	1
β-strand	156-163	8	2
α-helix	165-179	15
β-strand	183-189	7	2
β-strand	192-203	12	2
α-helix	205-215	11
β-strand	221-225	5	2
β-strand	226	1	1
α-helix	229-236	8
β-strand	241-246	6	2
α-helix	254-257	4
α-helix	259-260	2

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	130-133	4
α-helix	140-145	6
β-strand	146	1	3
β-strand	155-163	9	4
α-helix	165-179	15
β-strand	183-189	7	4
β-strand	192-204	13	4
α-helix	205-215	11
β-strand	221-225	5	4
β-strand	226	1	3
α-helix	229-236	8
β-strand	241-246	6	4
α-helix	254-257	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Large T antigen	A, B	protein	134	Simian virus 40	P03070 (AlphaFold model)
DNA (5'-d(gpapgpgpapgpgpcptptptptptptpgpgpapgpgpcp*c)-3')	X	DNA	21	synthetic construct
DNA (5'-d(apcptpcpcptpcpcpgpapapapapapapcpcptpcpcpgpgp*a)-3')	Y	DNA	23	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5D9I_1 Large T antigen (chains A, B)
GSKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHN
SYNHNILFFLTPHRHRVSAINNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESL
PGGLKEHDFNPESS

Sequence of entity 2 (X), FASTA

>5D9I_2 DNA (5'-D(*GP*AP*GP*GP*AP*GP*GP*CP*TP*TP*TP*TP*TP*TP*GP*GP*AP*GP*GP*CP*C)-3') (chains X)
GAGGAGGCTTTTTTGGAGGCC

Sequence of entity 3 (Y), FASTA

>5D9I_3 DNA (5'-D(*AP*CP*TP*CP*CP*TP*CP*CP*GP*AP*AP*AP*AP*AP*AP*CP*CP*TP*CP*CP*GP*GP*A)-3') (chains Y)
ACTCCTCCGAAAAAACCTCCGGA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (EDO, ACT) are not listed.

Primary citation

Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA. Meinke, G., Phelan, P.J., Fradet-Turcotte, A. et al. J Virol (2011) 85:818-827. DOI 10.1128/JVI.01738-10 · 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…
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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