7NSU: ColicinE9 intact translocation complex

ColicinE9 intact translocation complex. Determined by electron microscopy at 4.7 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 4.7 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 6
Atoms: 18,543
Mol. weight: 285.44 kDa
Released: 11 Aug 2021

Explore 7NSU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NSU contains 46 α-helices and 165 β-strands across 6 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: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	9-23	15	1
β-strand	31	1	2
β-strand	36-37	2	1
β-strand	40-49	10	1
β-strand	55-66	12	1
β-strand	80-90	11	1
β-strand	95-102	8	1
α-helix	104-109	6
β-strand	132-141	10	1
α-helix	143-146	4
β-strand	151-158	8	1
β-strand	173-182	10	1
β-strand	185-195	11	1
α-helix	198-201	4
β-strand	210-222	13	1
β-strand	225-235	11	1
β-strand	239-242	4	3
β-strand	247-250	4	3
β-strand	253-263	11	1
β-strand	265	1	1
β-strand	269	1	1
β-strand	272-283	12	1
β-strand	287-301	15	1
β-strand	307-316	10	1
β-strand	329	1	2
β-strand	331-339	9	1

Chain B: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	9-23	15	4
β-strand	31	1	5
β-strand	36-37	2	4
β-strand	40-49	10	4
β-strand	55-66	12	4
β-strand	80-90	11	4
β-strand	95-102	8	4
α-helix	104-109	6
β-strand	132-141	10	4
α-helix	143-146	4
β-strand	151-158	8	4
α-helix	166-168	3
β-strand	173-182	10	4
β-strand	185-195	11	4
α-helix	198-202	5
β-strand	210-222	13	4
β-strand	225-235	11	4
β-strand	239-242	4	6
β-strand	247-250	4	6
β-strand	253-263	11	4
β-strand	265	1	4
β-strand	269	1	4
β-strand	272-283	12	4
β-strand	287-302	16	4
β-strand	307-316	10	4
β-strand	329	1	5
β-strand	331-339	9	4

Chain C: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	9-23	15	7
β-strand	31	1	8
β-strand	36-37	2	7
β-strand	40-49	10	7
β-strand	55-66	12	7
β-strand	80-90	11	7
β-strand	95-102	8	7
α-helix	104-109	6
β-strand	132-141	10	7
α-helix	143-146	4
β-strand	151-158	8	7
β-strand	173-182	10	7
β-strand	185-195	11	7
α-helix	198-202	5
β-strand	210-222	13	7
β-strand	225-235	11	7
β-strand	239-242	4	9
β-strand	247-250	4	9
β-strand	253-263	11	7
β-strand	265	1	7
β-strand	269	1	7
β-strand	272-283	12	7
β-strand	287-301	15	7
β-strand	307-316	10	7
β-strand	329	1	8
β-strand	331-339	9	7

Chain D: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	54-55	2
α-helix	86-87	2
β-strand	88	1	10
α-helix	89	1
β-strand	94-96	3	11
β-strand	99	1	12
β-strand	102	1	12
β-strand	103-104	2	13
α-helix	111-113	3
α-helix	114-124	11
β-strand	133-139	7	14
α-helix	142-148	7
β-strand	155-161	7	11
α-helix	162-165	4
β-strand	179-191	13	14
β-strand	194-208	15	14
β-strand	209-211	3	11
β-strand	213-214	2	13
β-strand	220-224	5	13
β-strand	230-234	5	13
α-helix	240-241	2
β-strand	242	1	10
β-strand	246	1	15
β-strand	249	1	15
β-strand	250	1	14
β-strand	258-259	2	14
β-strand	268-274	7	11
α-helix	277-279	3
α-helix	281-283	3
β-strand	284-290	7	11
α-helix	294-312	19
α-helix	318-376	59
α-helix	377-381	5
α-helix	387-445	59

Chain E: 8 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	35-37	3	16
β-strand	38-39	2	17
α-helix	40-42	3
β-strand	43	1	17
α-helix	54-64	11
β-strand	68-70	3	16
α-helix	73-75	3
α-helix	88-92	5
β-strand	98-106	9	17
β-strand	112-120	9	17
β-strand	128-136	9	17
α-helix	138-140	3
α-helix	141-157	17
β-strand	166-172	7	18
β-strand	180-186	7	18
β-strand	193-198	6	18
β-strand	206-207	2	19
β-strand	213-218	6	19
β-strand	225-230	6	19
β-strand	236-240	5	19
β-strand	246-251	6	20
β-strand	257-262	6	20
β-strand	269-274	6	20
β-strand	280-282	3	20
β-strand	290-295	6	21
β-strand	301-306	6	21
β-strand	313-318	6	21
β-strand	325-326	2	21
β-strand	333-339	7	22
β-strand	345-352	8	22
β-strand	355-362	8	22
β-strand	368-370	3	22
β-strand	378-382	5	23
β-strand	388-392	5	23
α-helix	395-398	4
β-strand	401-405	5	23
β-strand	411-413	3	23
α-helix	414-417	4
β-strand	420-426	7	18

Chain F: 14 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	24
β-strand	17-18	2	24
α-helix	19-21	3
β-strand	26-30	5	25
α-helix	31-37	7
α-helix	42-46	5
β-strand	52-56	5	26
β-strand	64-68	5	26
α-helix	73-75	3
β-strand	77-80	4	25
β-strand	83-84	2	25
α-helix	88-91	4
α-helix	101-103	3
β-strand	106-111	6	25
α-helix	115-118	4
β-strand	125-130	6	25
β-strand	137-145	9	27
β-strand	149-159	11	27
β-strand	165-175	11	27
β-strand	197-208	12	27
β-strand	214-228	15	27
β-strand	234	1	28
β-strand	237	1	28
β-strand	242-257	16	27
β-strand	261-277	17	27
β-strand	289-304	16	27
β-strand	309-322	14	27
β-strand	325	1	29
α-helix	326-328	3
β-strand	329	1	29
β-strand	334-346	13	27
β-strand	353-362	10	27
β-strand	366-380	15	27
β-strand	383-394	12	27
α-helix	395-397	3
α-helix	398-402	5
α-helix	410-412	3
β-strand	413-426	14	27
β-strand	429-447	19	27
β-strand	452-472	21	27
β-strand	475-488	14	27
α-helix	493	1
β-strand	494	1	27
α-helix	495	1
β-strand	501-508	8	27
β-strand	511	1	30
β-strand	514	1	30
β-strand	515-523	9	27
β-strand	527-529	3	31
β-strand	538-540	3	31
α-helix	541-543	3
β-strand	544-554	11	27
β-strand	559-566	8	27
β-strand	576	1	32
β-strand	579	1	32
β-strand	585-593	9	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein F	A, B, C	protein	340	Escherichia coli (strain K12)	P02931 (AlphaFold model)
Colicin-E9	D	protein	582	Escherichia coli	P09883 (AlphaFold model)
Tol-Pal system protein TolB	E	protein	430	Escherichia coli (strain K12)	P0A855 (AlphaFold model)
Vitamin B12 transporter BtuB	F	protein	594	Escherichia coli (strain K12)	P06129 (AlphaFold model)

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

>7NSU_1 Outer membrane protein F (chains A, B, C)
AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQ
WEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGG
DTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISY
EYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPI
TNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGAT
YYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

Sequence of entity 2 (D), FASTA

>7NSU_2 Colicin-E9 (chains D)
MSGGDGRGHNTGAHSTSGNINGGPTGIGVSGGCSDGSGWSSENNPWGGGSGSGIHWGGGS
GRGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISASELSAAIAGII
AKLKKVNLKFTPFGVVLSSLIPSEIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATV
NVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNDSTP
AVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQR
QDEENRRQQEWDATHPVEAAERNYERARAELNQANEDVARNQERQAKAVQVYNSRKSELD
AANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKS
DADAALSAAQERRKQKENKEKDAKDKLDKESKRNKPGKATGKGKPVGDKWLDDAGKDSGA
PIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQ
VGGRKVYELHHDKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

Sequence of entity 3 (E), FASTA

>7NSU_3 Tol-Pal system protein TolB (chains E)
MKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAA
DLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVD
TGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPY
ELRVSDYDGYNQFVVHRSPQCLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVA
SFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQ
NLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAK
QDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQ
VKFPAWSPYL

Sequence of entity 4 (F), FASTA

>7NSU_4 Vitamin B12 transporter BtuB (chains F)
QDTSPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGS
GQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGS
DAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDV
VAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLL
DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQW
ANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSD
DNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEG
AFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVS
YDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVK
MGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF

Primary citation

Porin threading drives receptor disengagement and establishes active colicin transport through Escherichia coli OmpF. Francis, M.R., Webby, M.N., Housden, N.G. et al. EMBO J (2021) 40:e108610-e108610. DOI 10.15252/embj.2021108610 · PubMed

Other PDB entries of the same protein (UniProt P02931 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZFG 1.59 Å, Structure of OMPF PORIN
4GCS 1.87 Å, Crystal Structure of E. coli OmpF porin in complex with Ertapenem
3POQ 1.9 Å, Crystal structure of E.coli OmpF porin in lipidic cubic phase: space group H32, small…
4LSF 1.9 Å, Ion selectivity of OmpF soaked in 0.1M KBr
6ZHV 1.95 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4GCP 1.98 Å, Crystal Structure of E. coli OmpF porin in complex with Ampicillin
3POX 2.0 Å, Crystal Structure of E.coli OmpF porin in lipidic cubic phase: space group P1
6ZHP 2.05 Å, Crystal structure of OmpF porin soaked in ciprofloxacin metaloantibiotic
4LSI 2.09 Å, Ion selectivity of OmpF porin soaked in 0.3M KBr
4LSE 2.1 Å, Ion selectivity of OmpF porin soaked in 0.2M NaBr
1HXX 2.2 Å, Ompf porin mutant Y106F
4GCQ 2.2 Å, Crystal Structure of E. coli OmpF porin in complex with Carbenicillin

Browse structure collections

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