1PT3: Nuclease-ColE7

Crystal structures of nuclease-ColE7 complexed with octamer DNA. Determined by X-ray diffraction at 2.5 Å resolution. Released 30 Mar 2004.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Escherichia coli str. K12 substr.
Chains: 8
Atoms: 3,262
Mol. weight: 43.89 kDa
Released: 30 Mar 2004

Explore 1PT3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PT3 contains 19 α-helices and 26 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: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	1
β-strand	454	1	2
β-strand	458	1	3
α-helix	464-467	4
β-strand	474-475	2	4
β-strand	477	1	3
α-helix	478-484	7
β-strand	488-489	2	1
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-521	7
α-helix	525-527	3
β-strand	528	1	5
α-helix	531-533	3
β-strand	535	1	6
β-strand	538	1	6
β-strand	540	1	5
β-strand	542-545	4	4
β-strand	557	1	2
α-helix	558-560	3
β-strand	561-564	4	4
α-helix	566-574	9

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	7
β-strand	454	1	8
β-strand	458	1	9
α-helix	464-466	3
β-strand	474-475	2	10
β-strand	477	1	9
α-helix	478-484	7
β-strand	488-489	2	7
α-helix	492-504	13
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	11
α-helix	531-533	3
β-strand	535	1	12
β-strand	538	1	12
β-strand	540	1	11
β-strand	542-545	4	10
α-helix	549-551	3
β-strand	557	1	8
α-helix	558-560	3
β-strand	561-564	4	10
α-helix	566-572	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-gcgatcgc-3'	C, D, E, F, G, H	DNA	8
Colicin E7	A, B	protein	128	Escherichia coli str. K12 substr.	Q47112 (AlphaFold model)

Sequence of entity 1 (C, D, E, F, G, H), FASTA

>1PT3_1 5'-GCGATCGC-3' (chains C, D, E, F, G, H)
GCGATCGC

Sequence of entity 2 (A, B), FASTA

>1PT3_2 Colicin E7 (chains A, B)
KPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSKDPE
LSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKR
HIDIHRGK

Primary citation

DNA binding and degradation by the HNH protein ColE7. Hsia, K.C., Chak, K.F., Liang, P.H. et al. Structure (2004) 12:205-214. DOI 10.1016/S0969-2126(04)00006-1 · PubMed

Other PDB entries of the same protein (UniProt Q47112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2AXC 1.7 Å, Crystal structure of ColE7 translocation domain
3ZFK 1.7 Å, N-terminal truncated Nuclease Domain of Colicin E7
2JB0 1.91 Å, Crystal structure of the mutant H573A of the nuclease domain of COLE7 in complex with IM7
1MZ8 2.0 Å, Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion…
1ZNV 2.0 Å, How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal…
2ERH 2.0 Å, Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7…
2JAZ 2.03 Å, Crystal structure of the mutant N560D of the nuclease domain of COLE7 in complex with IM7
1M08 2.1 Å, Crystal structure of the unbound nuclease domain of ColE7
1UJZ 2.1 Å, Crystal structure of the E7_C/Im7_C complex; a computationally designed interface…
2JBG 2.2 Å, crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7
3GKL 2.2 Å, Following evolutionary paths to high affinity and selectivity protein-protein…
7CEI 2.3 Å, The endonuclease domain of colicin E7 in complex with its inhibitor IM7 protein

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