1ZNV: Colicin E7 immunity protein

How a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Mar 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Escherichia coli str. K12 substr.
Chains: 4
Atoms: 3,763
Mol. weight: 52.58 kDa
Ligands: NI, PO4
Released: 14 Mar 2006

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

Secondary structure: helices and β-sheets

1ZNV contains 30 α-helices and 26 β-strands across 4 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	12-26	15
α-helix	32-45	14
α-helix	52-55	4
α-helix	65-78	14

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	1
β-strand	453-454	2	2
β-strand	458	1	3
α-helix	464-467	4
β-strand	474-475	2	4
α-helix	476	1
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	515-522	8
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	556-557	2	2
α-helix	558-560	3
β-strand	561-564	4	4
α-helix	566-573	8

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	12-26	15
α-helix	32-45	14
α-helix	52-55	4
α-helix	65-78	14
α-helix	84-86	3

Chain D: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	452	1	7
β-strand	453-454	2	8
β-strand	458	1	9
α-helix	464-467	4
β-strand	474-475	2	10
α-helix	476	1
β-strand	477	1	9
α-helix	478-484	7
β-strand	488	1	7
α-helix	492-505	14
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
β-strand	556-557	2	8
β-strand	561-564	4	10
α-helix	566-572	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin E7 immunity protein	A, C	protein	93	Escherichia coli str. K12 substr.	Q03708 (AlphaFold model)
Colicin E7	B, D	protein	134	Escherichia coli str. K12 substr.	Q47112 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1ZNV_1 Colicin E7 immunity protein (chains A, C)
MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDN
RDDSPEGIVKEIKEWRAANGKPGFKQGHHHHHH

Sequence of entity 2 (B, D), FASTA

>1ZNV_2 Colicin E7 (chains B, D)
MESKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEE
VSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHEEKPISQNGGVYDMDNIS
VVTPKRHIDIHRGK

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	2
PO4	Phosphate ion	O4 P	2

Primary citation

Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+. Doudeva, L.G., Huang, H., Hsia, K.C. et al. Protein Sci (2006) 15:269-280. DOI 10.1110/ps.051903406 · PubMed

Other PDB entries of the same protein (UniProt Q03708 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WNW 1.79 Å, Chaperone Spy bound to Im7 6-45 ensemble
1CEI 1.8 Å, Structure determination of the colicin E7 immunity protein (IMME7) that binds…
1UNK 1.8 Å, Structure of colicin E7 immunity protein
2JB0 1.91 Å, Crystal structure of the mutant H573A of the nuclease domain of COLE7 in complex with IM7
1AYI 2.0 Å, Colicin E7 immunity protein IM7
1MZ8 2.0 Å, Crystal structures of the nuclease domain of COLE7/IM7 in complex with a phosphate ion…
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
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
7CEI 2.3 Å, The endonuclease domain of colicin E7 in complex with its inhibitor IM7 protein
4F37 2.57 Å, Structure of the tethered N-terminus of Alzheimer's disease A peptide

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