3GKL: Colicin-E9 immunity protein

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins. Determined by X-ray diffraction at 2.2 Å resolution. Released 8 Sept 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Escherichia coli
Chains: 4
Atoms: 3,223
Mol. weight: 51.6 kDa
Ligands: ZN
Released: 8 Sept 2009

Explore 3GKL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3GKL contains 31 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: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	453-454	2	1
β-strand	458	1	2
α-helix	464-467	4
β-strand	474-475	2	3
α-helix	476	1
β-strand	477	1	2
α-helix	478-484	7
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-522	8
β-strand	528	1	4
α-helix	529-530	2
β-strand	535	1	5
β-strand	538	1	5
β-strand	540	1	4
β-strand	542-545	4	3
β-strand	556-557	2	1
α-helix	558-560	3
β-strand	561-564	4	3
α-helix	566-572	7

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	452	1	6
β-strand	453-454	2	7
β-strand	458	1	8
α-helix	464-469	6
β-strand	474-475	2	9
α-helix	476	1
β-strand	477	1	8
α-helix	478-484	7
β-strand	488	1	6
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	10
α-helix	529-530	2
α-helix	531-533	3
β-strand	535	1	11
β-strand	538	1	11
β-strand	540	1	10
β-strand	542-545	4	9
β-strand	556-557	2	7
β-strand	561-564	4	9
α-helix	566-573	8

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1007-1009	3
β-strand	1011	1	12
α-helix	1012-1022	11
α-helix	1030-1044	15
α-helix	1051-1054	4
α-helix	1064-1076	13
β-strand	1084	1	12

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	1007-1009	3
α-helix	1012-1022	11
α-helix	1025-1027	3
α-helix	1030-1044	15
α-helix	1051-1054	4
α-helix	1064-1070	7
α-helix	1074-1077	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E9 immunity protein	A, B	protein	141	Escherichia coli	Q47112 (AlphaFold model)
Colicin-E7	C, D	protein	86	Escherichia coli	P13479 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3GKL_1 Colicin-E9 immunity protein (chains A, B)
MHHHHHHSMGKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDF
RKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEKPISQNGGV
YDMDNISVVTPKRHIDIHRGK

Sequence of entity 2 (C, D), FASTA

>3GKL_2 Colicin-E7 (chains C, D)
MELKHSISDYTEAEFLQLVATICDADATSEEELDKLITHFGEMTEHPSGSDLIYYPEEGD
DDSPSGIVNTVKQWRAANGKSGFKQG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Following evolutionary paths to high affinity and selectivity protein-protein interactions. Bernath, K., Dym, O., Albeck, S. et al. To be published.

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
7CEI 2.3 Å, The endonuclease domain of colicin E7 in complex with its inhibitor IM7 protein
3GJN 2.48 Å, Following evolutionary paths to high affinity and selectivity protein-protein…

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