5EW5: Colicin E9

Crystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9. Determined by X-ray diffraction at 3.2 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Escherichia coli
Chains: 8
Atoms: 17,397
Mol. weight: 288.91 kDa
Released: 20 Jul 2016

Explore 5EW5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EW5 contains 110 α-helices and 145 β-strands across 8 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: 22 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	86-87	2
β-strand	88	1	1
α-helix	89	1
β-strand	94-96	3	2
β-strand	99	1	3
β-strand	102	1	3
β-strand	103-104	2	4
β-strand	107	1	5
α-helix	111-113	3
α-helix	114-124	11
β-strand	133-136	4	6
β-strand	139-140	2	7
α-helix	142-148	7
β-strand	155-161	7	2
α-helix	162-164	3
β-strand	179-191	13	6
β-strand	194-208	15	6
β-strand	209-211	3	2
β-strand	213-214	2	4
β-strand	221-224	4	4
β-strand	230-233	4	4
β-strand	235	1	5
α-helix	240-241	2
β-strand	242	1	1
β-strand	249-250	2	7
β-strand	258-259	2	6
β-strand	268-274	7	2
α-helix	277-279	3
α-helix	281-283	3
β-strand	284-290	7	2
α-helix	294-313	20
α-helix	316-375	60
α-helix	376-381	6
α-helix	387-452	66
β-strand	457-458	2	8
β-strand	460	1	9
β-strand	464	1	10
α-helix	470-473	4
β-strand	480-481	2	11
β-strand	483	1	10
α-helix	484-490	7
β-strand	494-495	2	8
α-helix	498-510	13
α-helix	516-518	3
α-helix	521-528	8
α-helix	531-533	3
β-strand	534	1	12
α-helix	535-536	2
α-helix	537-539	3
β-strand	541	1	13
β-strand	544	1	13
β-strand	546	1	12
β-strand	548-551	4	11
β-strand	563	1	9
β-strand	567-570	4	11
α-helix	572-578	7

Chain B: 24 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	86-87	2
β-strand	88	1	14
α-helix	89	1
β-strand	94-96	3	15
β-strand	99	1	16
β-strand	102	1	16
β-strand	103-107	5	17
α-helix	111-113	3
α-helix	114-124	11
β-strand	133-140	8	18
α-helix	142-148	7
β-strand	155-161	7	15
α-helix	162-165	4
β-strand	179-182	4	19
β-strand	185-191	7	18
β-strand	194-201	8	18
β-strand	205-208	4	19
β-strand	209-211	3	15
β-strand	213-214	2	17
β-strand	220-223	4	17
β-strand	231-235	5	17
α-helix	240-241	2
β-strand	242	1	14
β-strand	246	1	18
β-strand	249-250	2	18
β-strand	258-259	2	18
β-strand	268-274	7	15
α-helix	277-279	3
α-helix	281-283	3
β-strand	284-290	7	15
α-helix	294-313	20
α-helix	316-375	60
α-helix	376-381	6
α-helix	387-450	64
α-helix	452-454	3
β-strand	457-458	2	20
β-strand	460	1	21
β-strand	464	1	22
α-helix	470-473	4
β-strand	480-481	2	23
α-helix	482	1
β-strand	483	1	22
α-helix	484-490	7
β-strand	494-495	2	20
α-helix	498-510	13
α-helix	516-518	3
α-helix	521-527	7
α-helix	531-533	3
β-strand	534	1	24
α-helix	535-536	2
α-helix	537-539	3
β-strand	541	1	25
β-strand	544	1	25
β-strand	546	1	24
β-strand	548-551	4	23
β-strand	563	1	21
β-strand	567-570	4	23
α-helix	572-578	7

Chain C: 23 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	88-90	3	26
β-strand	94-96	3	27
β-strand	99	1	28
β-strand	102	1	28
β-strand	103-112	10	26
α-helix	114-122	9
β-strand	133-136	4	29
β-strand	139-140	2	30
α-helix	142-146	5
β-strand	155-157	3	27
β-strand	158-161	4	31
α-helix	162-164	3
β-strand	166	1	32
α-helix	170-172	3
β-strand	179-182	4	32
β-strand	185-186	2	29
β-strand	189-191	3	30
β-strand	194-196	3	30
β-strand	198-201	4	29
β-strand	205-208	4	32
β-strand	209-211	3	31
β-strand	213-214	2	26
β-strand	221-224	4	26
β-strand	226	1	33
β-strand	228	1	33
α-helix	229	1
β-strand	230-235	6	26
α-helix	240-242	3
β-strand	249-250	2	30
β-strand	258-259	2	29
α-helix	260-261	2
β-strand	268-274	7	31
α-helix	275-276	2
β-strand	284-289	6	31
β-strand	290	1	27
α-helix	294-314	21
α-helix	316-375	60
α-helix	377-379	3
α-helix	386-450	65
α-helix	451-454	4
β-strand	457-458	2	34
β-strand	460	1	35
β-strand	464	1	36
α-helix	470-473	4
β-strand	477	1	37
β-strand	479	1	37
β-strand	480-481	2	38
α-helix	482	1
β-strand	483	1	36
α-helix	484-490	7
β-strand	494-495	2	34
α-helix	498-510	13
α-helix	521-527	7
α-helix	531-533	3
β-strand	534	1	39
α-helix	535-536	2
α-helix	537-539	3
β-strand	541	1	40
β-strand	544	1	40
β-strand	546	1	39
β-strand	548-551	4	38
α-helix	555-557	3
β-strand	563	1	35
β-strand	567-570	4	38
α-helix	572-578	7

Chain D: 21 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	88-90	3	41
β-strand	94-96	3	42
β-strand	99	1	43
β-strand	102	1	43
β-strand	103-112	10	41
α-helix	114-122	9
β-strand	133-140	8	44
α-helix	142-146	5
β-strand	155-161	7	42
α-helix	162-164	3
β-strand	166	1	45
α-helix	170-172	3
β-strand	179-182	4	45
β-strand	185-191	7	44
β-strand	194-201	8	44
β-strand	205-208	4	45
β-strand	209-211	3	42
β-strand	213-214	2	41
β-strand	221-224	4	41
β-strand	226	1	46
β-strand	228	1	46
β-strand	230-236	7	41
α-helix	240-242	3
β-strand	249-250	2	44
β-strand	258-259	2	44
β-strand	268-274	7	42
α-helix	275-276	2
β-strand	284-290	7	42
α-helix	294-314	21
α-helix	316-375	60
α-helix	377-379	3
α-helix	386-450	65
α-helix	451-454	4
β-strand	457-458	2	47
β-strand	460	1	48
β-strand	464	1	49
α-helix	470-473	4
β-strand	480-481	2	50
α-helix	482	1
β-strand	483	1	49
α-helix	484-490	7
β-strand	494-495	2	47
α-helix	498-511	14
α-helix	521-527	7
α-helix	531-533	3
β-strand	534	1	51
α-helix	535-536	2
α-helix	537-539	3
β-strand	541	1	52
β-strand	544	1	52
β-strand	546	1	51
β-strand	548-551	4	50
α-helix	555-557	3
β-strand	563	1	48
β-strand	567-570	4	50
α-helix	572-578	7

Chains E and F: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	12-24	13
α-helix	30-44	15
α-helix	51-54	4
α-helix	56-57	2
α-helix	64-77	14

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-9	3
α-helix	12-24	13
α-helix	30-44	15
α-helix	51-54	4
α-helix	64-77	14

Chain H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	12-24	13
α-helix	30-44	15
α-helix	64-74	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Colicin-E9	A, B, C, D	protein	582	Escherichia coli	P09883 (AlphaFold model)
Colicin-E9 immunity protein	E, F, G, H	protein	94	Escherichia coli	P13479 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5EW5_1 Colicin-E9 (chains A, B, C, D)
MSGGDGRGHNTGAHSTSGNINGGPTGIGVSGGASDGSGWSSENNPWGGGSGSGIHWGGGS
GRGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISASELSAAIAGII
AKLKKVNLKFTPFGVVLSSLIPSEIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATV
NVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNDSTP
AVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQR
QDEENRRQQEWDATHPVEAAERNCERARAELNQANEDVARNQERQAKAVQVYNSRKSELD
AANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKS
DADAALSAAQERRKQKENKEKDAKDKCAMESKRNKPGKATGKGKPVGDKWLDDAGKDSGA
PIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQ
VGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

Sequence of entity 2 (E, F, G, H), FASTA

>5EW5_2 Colicin-E9 immunity protein (chains E, F, G, H)
MELKHSISDYTEAEFLQLVTTICNADTSSEEELVKLVTHFEEMTEHPSGSDLIYYPKEGD
DDSPSGIVNTVKQWRAANGKSGFKQGLEHHHHHH

Primary citation

Structural and biophysical analysis of nuclease protein antibiotics. Klein, A., Wojdyla, J.A., Joshi, A. et al. Biochem J (2016) 473:2799-2812. DOI 10.1042/BCJ20160544 · PubMed

Other PDB entries of the same protein (UniProt P09883 (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)
2WPT 1.78 Å, The crystal structure of Im2 in complex with colicin E9 DNase
1FSJ 1.8 Å, Crystal structure of the E9 DNase domain
2GZE 1.8 Å, Crystal structure of the E9 DNase domain with a mutant immunity protein IM9 (Y55A)

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