3GJN: 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 2.48 Å resolution. Released 15 Sept 2009.

Method: X-ray diffraction
Resolution: 2.48 Å
Organism: Escherichia coli
Chains: 4
Atoms: 3,243
Mol. weight: 51.88 kDa
Ligands: ZN
Released: 15 Sept 2009

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

Secondary structure: helices and β-sheets

3GJN contains 33 α-helices and 32 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: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	1007-1009	3
β-strand	1011	1	1
α-helix	1012-1022	11
β-strand	1025	1	2
β-strand	1028	1	2
α-helix	1030-1044	15
α-helix	1051-1054	4
α-helix	1056-1057	2
α-helix	1064-1077	14
β-strand	1084	1	1

Chain B: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	454	1	3
β-strand	458	1	4
α-helix	464-467	4
β-strand	474-475	2	5
α-helix	476	1
β-strand	477	1	4
α-helix	478-484	7
α-helix	492-503	12
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	6
α-helix	529-530	2
α-helix	531-533	3
β-strand	535	1	7
β-strand	538	1	7
β-strand	540	1	6
β-strand	542-545	4	5
β-strand	557	1	3
α-helix	558-560	3
β-strand	561-564	4	5
α-helix	566-573	8

Chain C: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451	1	8
β-strand	454	1	9
β-strand	458	1	10
α-helix	464-469	6
β-strand	474-475	2	11
α-helix	476	1
β-strand	477	1	10
α-helix	478-484	7
β-strand	489	1	8
α-helix	492-505	14
α-helix	507-510	4
α-helix	515-522	8
α-helix	525-527	3
β-strand	528	1	12
α-helix	529-530	2
α-helix	531-533	3
β-strand	535	1	13
β-strand	538	1	13
β-strand	540	1	12
β-strand	542-545	4	11
β-strand	557	1	9
α-helix	558-560	3
β-strand	561-564	4	11
α-helix	566-573	8

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	1007-1009	3
β-strand	1011	1	14
α-helix	1012-1022	11
β-strand	1025	1	15
β-strand	1028	1	15
α-helix	1030-1044	15
α-helix	1051-1054	4
α-helix	1064-1077	14
β-strand	1084	1	14

Molecules and chains

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

Sequence of entity 1 (A, D), FASTA

>3GJN_1 Colicin-E9 immunity protein (chains A, D)
MELKHSISDYTEAEFLQLVTTICDAEATSEEELDKLITHFEEMTEHPSGSDLIYWPKEGD
DDSPSGIVNTVKQWRAANGKSGFKQG

Sequence of entity 2 (B, C), FASTA

>3GJN_2 Colicin-E7 (chains B, C)
MHHHHHHSMGKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDF
RKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHAEKPISQNGGV
YDMDNISVVTPKRHIDIHRGK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Following evolutionary paths to protein-protein interactions with high affinity and selectivity. Levin, K.B., Dym, O., Albeck, S. et al. Nat Struct Mol Biol (2009) 16:1049-1055. DOI 10.1038/nsmb.1670 · PubMed

Other PDB entries of the same protein (UniProt P13479 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FR2 1.6 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9(E41A)
2GYK 1.6 Å, Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity…
2GZJ 1.6 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (D51A)
2VLN 1.6 Å, N75A mutant of E9 DNase domain in complex with Im9
2VLQ 1.6 Å, F86A mutant of E9 DNase domain in complex with Im9
1EMV 1.7 Å, Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7 Å)
2GZG 1.7 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (Y55F)
2GZI 1.7 Å, Crystal Structure of the E9 DNase Domain with a Mutant Immunity Protein IM9 (V34A)
2GZF 1.75 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y54F)
2GZE 1.8 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A)
2VLO 1.8 Å, K97A mutant of E9 DNase domain in complex with Im9
2VLP 2.0 Å, R54A mutant of E9 DNase domain in complex with Im9

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