7NST: ColicinE9 partial translocation complex

ColicinE9 partial translocation complex. Determined by electron microscopy at 3.7 Å resolution. Released 11 Aug 2021.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 5
Atoms: 12,946
Mol. weight: 188.91 kDa
Released: 11 Aug 2021

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

Secondary structure: helices and β-sheets

7NST contains 29 α-helices and 123 β-strands across 5 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.

Chains A, B and C: 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	40-50	11	1
β-strand	55-66	12	1
β-strand	80-90	11	1
β-strand	95-101	7	1
α-helix	104-110	7
β-strand	133-141	9	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	198-202	5
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	287-304	18	1
β-strand	307-316	10	1
β-strand	329	1	2
β-strand	331-339	9	1

Chain D: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
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
β-strand	107	1	14
α-helix	111-113	3
α-helix	114-124	11
β-strand	133-139	7	15
α-helix	142-148	7
β-strand	155-161	7	11
α-helix	162-165	4
β-strand	179-191	13	15
β-strand	194-208	15	15
β-strand	209-211	3	11
β-strand	213-214	2	13
β-strand	221-223	3	13
β-strand	231-233	3	13
β-strand	235	1	14
α-helix	240-241	2
β-strand	242	1	10
β-strand	250	1	15
β-strand	258-259	2	15
β-strand	268-274	7	11
α-helix	277-279	3
α-helix	281-283	3
β-strand	284-290	7	11
α-helix	294-313	20

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	166-173	8	18
β-strand	180-186	7	18
β-strand	193-198	6	18
β-strand	202-207	6	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	291-295	5	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	419-426	8	18

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	314	Escherichia coli	P09883 (AlphaFold model)
Tol-Pal system protein TolB	E	protein	430	Escherichia coli (strain K12)	P0A855 (AlphaFold model)

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

>7NST_1 Outer membrane protein F (chains A, B, C)
AEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQ
WEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGG
DTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISY
EYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPI
TNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGAT
YYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF

Sequence of entity 2 (D), FASTA

>7NST_2 Colicin-E9 (chains D)
MSGGDGRGHNTGAHSTSGNINGGPTGIGVSGGCSDGSGWSSENNPWGGGSGSGIHWGGGS
GRGNGGGNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISASELSAAIAGII
AKLKKVNLKFTPFGVVLSSLIPSEIAKDDPNMMSKIVTSLPADDITESPVSSLPLDKATV
NVNVRVVDDVKDERQNISVVSGVPMSVPVVDAKPTERPGVFTASIPGAPVLNISVNDSTP
AVQTLSPGVTNNTDKDVRPAGFTQGGNTRDAVIRFPKDSGHNAVYVSVSDVLSPDQVKQR
QDEENRRQQEWDAT

Sequence of entity 3 (E), FASTA

>7NST_3 Tol-Pal system protein TolB (chains E)
MKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAA
DLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVD
TGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPY
ELRVSDYDGYNQFVVHRSPQCLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVA
SFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQ
NLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAK
QDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQ
VKFPAWSPYL

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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