7NRI: Darobactin-bound E. coli BAM complex

Structure of the darobactin-bound E. coli BAM complex (BamABCDE). Determined by electron microscopy at 3.03 Å resolution. Released 21 Apr 2021.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Escherichia coli (strain K12), synthetic construct
Chains: 6
Atoms: 11,792
Mol. weight: 201.8 kDa
Released: 21 Apr 2021

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

Secondary structure: helices and β-sheets

7NRI contains 37 α-helices and 96 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: 19 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29-32	4	2
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-68	13
β-strand	72-79	8	2
β-strand	84-90	7	2
α-helix	91-92	2
β-strand	93-100	8	3
α-helix	107-117	11
β-strand	124	1	3
α-helix	130-144	15
β-strand	150-158	9	3
β-strand	162-170	9	3
β-strand	176-183	8	4
α-helix	190-194	5
α-helix	216-231	16
β-strand	239-247	9	4
β-strand	253-261	9	4
α-helix	262-265	4
β-strand	267-276	10	5
β-strand	294-295	2	5
α-helix	296	1
α-helix	298-314	17
β-strand	321-329	9	5
β-strand	334-342	9	5
β-strand	348-355	8	6
α-helix	362-366	5
α-helix	372	1
β-strand	376	1	6
α-helix	379-392	14
β-strand	395-405	11	6
β-strand	408-420	13	6
β-strand	425-433	9	7
β-strand	437-446	10	7
β-strand	456-463	8	7
β-strand	466-472	7	7
β-strand	475	1	7
β-strand	484-485	2	7
β-strand	488-495	8	7
α-helix	497-499	3
β-strand	501	1	8
β-strand	505-518	14	7
β-strand	523-537	15	7
β-strand	542	1	9
α-helix	543-551	9
β-strand	565-579	15	7
β-strand	590-600	11	7
α-helix	601	1
β-strand	608-620	13	7
β-strand	628-640	13	7
β-strand	652	1	10
β-strand	654	1	11
β-strand	662-663	2	12
β-strand	668	1	11
β-strand	671	1	8
β-strand	674	1	9
α-helix	692-694	3
β-strand	700	1	9
β-strand	705	1	8
β-strand	708	1	10
β-strand	710-720	11	7
α-helix	730-732	3
β-strand	734-745	12	7
β-strand	767-778	12	7
β-strand	781-788	8	7
β-strand	792	1	7
α-helix	797-798	2
β-strand	799-800	2	12
β-strand	802-806	5	7

Chain B: 2 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	44	1	13
β-strand	48-50	3	14
β-strand	71-75	5	15
β-strand	80-85	6	15
β-strand	91-96	6	15
β-strand	111	1	16
β-strand	116-117	2	17
β-strand	122-125	4	17
β-strand	126	1	16
β-strand	130-134	5	17
β-strand	141-146	6	17
β-strand	151	1	18
β-strand	156-158	3	19
β-strand	161-165	5	19
β-strand	166	1	18
β-strand	170-175	6	19
β-strand	183-186	4	19
β-strand	192-194	3	4
α-helix	198-200	3
β-strand	201-203	3	20
β-strand	206-211	6	20
β-strand	215-220	6	20
β-strand	226-231	6	20
β-strand	252-254	3	21
β-strand	257-260	4	21
β-strand	266-271	6	21
β-strand	277-282	6	21
β-strand	290-292	3	22
β-strand	295-299	5	22
β-strand	305-309	5	22
β-strand	315-319	5	22
β-strand	331-333	3	23
β-strand	336-339	4	23
β-strand	345-349	5	23
β-strand	356-361	6	23
β-strand	367	1	24
β-strand	372-374	3	14
β-strand	377-381	5	14
β-strand	382	1	24
β-strand	387-390	4	14
β-strand	392	1	13

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	32-34	3
α-helix	45-47	3
α-helix	49-51	3

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	32-43	12
α-helix	48-60	13
α-helix	68-81	14
α-helix	85-98	14
α-helix	103-105	3
α-helix	106-120	15
α-helix	138-153	16
α-helix	161-188	28
α-helix	192-204	13
α-helix	209-212	4
α-helix	215-224	10
α-helix	228-239	12

Chain E: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	25
α-helix	52-58	7
β-strand	72-80	9	25
β-strand	87-94	8	25
β-strand	103-107	5	25

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	788	Escherichia coli (strain K12)	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	381	Escherichia coli (strain K12)	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	320	Escherichia coli (strain K12)	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	226	Escherichia coli (strain K12)	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	102	Escherichia coli (strain K12)	P0A937
3-pyridin-4-yl-2,4-dihydro-INDENO[1,2-.c.]pyrazole	G	protein	7	synthetic construct

Sequence of entity 1 (A), FASTA

>7NRI_1 Outer membrane protein assembly factor BamA (chains A)
AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRD
GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDF
YYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLR
DEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNI
TEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP
RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSD
LVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSF
QAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDAD
LSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD
QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVP
IDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQAS
NYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWD
MGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE
QFQFNIGK

Sequence of entity 2 (B), FASTA

>7NRI_2 Outer membrane protein assembly factor BamB (chains B)
CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAG
LVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDG
TVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESA
PTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF
ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQ
SDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLL
IQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>7NRI_3 Outer membrane protein assembly factor BamC (chains C)
CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRP
PAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTD
WVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNV
ISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM
KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGH
TLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>7NRI_4 Outer membrane protein assembly factor BamD (chains D)
CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY
YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQH
ARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE
GMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 5 (E), FASTA

>7NRI_5 Outer membrane protein assembly factor BamE (chains E)
CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQ
QPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNKLHHHHHH

Sequence of entity 6 (G), FASTA

>7NRI_6 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE (chains G)
WNXSKSF

Primary citation

The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase. Kaur, H., Jakob, R.P., Marzinek, J.K. et al. Nature (2021) 593:125-129. DOI 10.1038/s41586-021-03455-w · PubMed

Other PDB entries of the same protein (UniProt P0A940 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3Q6B 1.5 Å, The high-resolution and new form crystal structure of BamA POTRA4-5 from E.coli
9CS2 1.78 Å, E. coli BamA beta-barrel bound to cyclic peptide CP3
6QGW 1.94 Å, Crystal structure of E.coli BamA beta-barrel in complex with nanobody E6
9CS0 1.94 Å, E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP1
9CS1 2.15 Å, E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2
4XGA 2.15 Å, Crystal structure of BamB and BamA P3-5 complex from E.coli
2QDF 2.2 Å, Structure of N-terminal domain of E. Coli YaeT
6QGX 2.2 Å, Crystal structure of E.coli BamA beta-barrel in complex with nanobody F7
7NRF 2.2 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)
7NRE 2.3 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)
7P1C 2.5 Å, Crystal structure of E.coli BamA beta-barrel in complex with darobactin B
7R1V 2.5 Å, Crystal structure of E.coli BamA beta-barrel in complex with dynobactin A

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