2A0I: F Factor TraI Relaxase Domain

F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA. Determined by X-ray diffraction at 2.72 Å resolution. Released 25 Oct 2005.

Method: X-ray diffraction
Resolution: 2.72 Å
Organism: Escherichia coli
Chains: 2
Atoms: 2,524
Mol. weight: 43.35 kDa
Ligands: MG
Released: 25 Oct 2005

Explore 2A0I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2A0I contains 16 α-helices and 15 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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
α-helix	10-16	7
β-strand	32-34	3	1
α-helix	36-40	5
α-helix	49-57	9
β-strand	59	1	2
β-strand	65	1	2
β-strand	70	1	3
β-strand	74	1	3
β-strand	79-85	7	1
α-helix	86-87	2
α-helix	88-95	8
α-helix	100-117	18
α-helix	118-120	3
β-strand	122-123	2	4
β-strand	134-135	2	4
β-strand	141-148	8	1
β-strand	154-163	10	1
β-strand	167	1	5
β-strand	172	1	5
α-helix	185-191	7
α-helix	193-210	18
β-strand	216-217	2	6
α-helix	220-222	3
β-strand	224-225	2	6
α-helix	231-234	4
α-helix	236-244	9
α-helix	251-260	10
α-helix	262-266	5
α-helix	270-282	13
α-helix	288-303	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
F plasmid single-stranded oriT DNA	B	DNA	22
TraI protein	A	protein	330	Escherichia coli	P14565 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>2A0I_1 F plasmid single-stranded oriT DNA (chains B)
TGGGGTGTGGTGCTTTTGGTGG

Sequence of entity 2 (A), FASTA

>2A0I_2 TraI protein (chains A)
MMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRL
PDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL
ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKV
GKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQT
IREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD
LRTLTPGPASQDGPDVQQAVTQAIAGLSER

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (IMD) are not listed.

Primary citation

Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase. Larkin, C., Datta, S., Harley, M.J. et al. Structure (2005) 13:1533-1544. DOI 10.1016/j.str.2005.06.013 · PubMed

Other PDB entries of the same protein (UniProt P14565 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FLD 2.4 Å, Crystal structure of the trai c-terminal domain
2Q7T 2.42 Å, Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base
1P4D 2.6 Å, F factor TraI Relaxase Domain
9F10 2.94 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, without accessory…
2Q7U 3.0 Å, Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base…
9F0Z 3.42 Å, CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode,…
9F12 3.42 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_-3ds-2_+143 and TraI…
9F0Y 3.45 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the…
9F11 3.68 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI…
9F0X 3.78 Å, CryoEM structure of the F plasmid relaxosome in its pre-initiation state, derived from…
2L8B TraI (381-569)

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