2JBG: Mutant N560A of the nuclease domain of ColE7

crystal structure of the mutant N560A of the nuclease domain of ColE7 in complex with Im7. Determined by X-ray diffraction at 2.2 Å resolution. Released 3 Apr 2007.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: ESCHERICHIA COLI
Chains: 4
Atoms: 3,678
Mol. weight: 50.18 kDa
Ligands: ZN
Released: 3 Apr 2007

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

Secondary structure: helices and β-sheets

2JBG contains 27 α-helices and 30 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	1
β-strand	454	1	2
β-strand	458	1	3
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	557	1	2
β-strand	561-564	4	4
α-helix	566-573	8

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	11	1	7
α-helix	12-26	15
α-helix	32-45	14
α-helix	52-55	4
α-helix	65-78	14
β-strand	85	1	7

Chain D: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	451-452	2	8
β-strand	453	1	9
β-strand	454	1	10
β-strand	458	1	11
α-helix	464-467	4
β-strand	474-475	2	12
α-helix	476	1
β-strand	477	1	11
α-helix	478-484	7
β-strand	485	1	9
β-strand	488-489	2	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	13
α-helix	531-533	3
β-strand	535	1	14
β-strand	538	1	14
β-strand	540	1	13
β-strand	542-545	4	12
β-strand	557	1	10
β-strand	561-564	4	12
α-helix	566-572	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E7 immunity protein	A, C	protein	87	ESCHERICHIA COLI	Q03708 (AlphaFold model)
Colicin E7	B, D	protein	131	ESCHERICHIA COLI	Q47112 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2JBG_1 COLICIN-E7 IMMUNITY PROTEIN (chains A, C)
MELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDN
RDDSPEGIVKEIKEWRAANGKPGFKQG

Sequence of entity 2 (B, D), FASTA

>2JBG_2 COLICIN E7 (chains B, D)
KRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFDDFRKKFWEEVSK
DPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDAISVVT
PKRHIDIHRGK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

The Conserved Asparagine in the Hnh Motif Serves an Important Structural Role in Metal Finger Endonucleases. Huang, H., Yuan, H.S. J Mol Biol (2007) 368:812. DOI 10.1016/J.JMB.2007.02.044 · 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…
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
1UJZ 2.1 Å, Crystal structure of the E7_C/Im7_C complex; a computationally designed interface…
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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