7R1W: E. coli BAM complex

E. coli BAM complex (BamABCDE) bound to dynobactin A. Determined by electron microscopy at 3.6 Å resolution. Released 28 Sept 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Escherichia coli K-12, Photorhabdus australis
Chains: 6
Atoms: 11,823
Mol. weight: 212.85 kDa
Released: 28 Sept 2022

Explore 7R1W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R1W contains 40 α-helices and 100 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: 21 helices, 54 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	146	1	4
β-strand	150-158	9	3
β-strand	162-170	9	3
β-strand	174	1	4
β-strand	176-183	8	5
α-helix	190-194	5
α-helix	216-231	16
β-strand	239-247	9	5
β-strand	253-261	9	5
α-helix	262-265	4
β-strand	267-276	10	6
α-helix	281-285	5
β-strand	294-295	2	6
α-helix	296	1
α-helix	298-314	17
β-strand	321-329	9	6
β-strand	334-342	9	6
β-strand	348-355	8	7
α-helix	362-366	5
α-helix	372	1
β-strand	376	1	7
α-helix	379-392	14
β-strand	395-405	11	7
β-strand	408-420	13	7
β-strand	426-433	8	8
β-strand	437-446	10	8
β-strand	456-463	8	8
β-strand	466-472	7	8
β-strand	475	1	8
β-strand	484-485	2	8
β-strand	488-495	8	8
α-helix	497-499	3
β-strand	501	1	9
β-strand	505-518	14	8
β-strand	523-537	15	8
β-strand	542	1	10
α-helix	543-549	7
α-helix	550-552	3
β-strand	564-579	16	8
β-strand	590-600	11	8
α-helix	601	1
β-strand	608-620	13	8
β-strand	628-640	13	8
β-strand	652	1	11
β-strand	654	1	12
β-strand	662-663	2	13
β-strand	668	1	12
β-strand	671	1	9
β-strand	674	1	10
α-helix	692-694	3
β-strand	700	1	10
β-strand	705	1	9
β-strand	708	1	11
β-strand	710-720	11	8
α-helix	730-732	3
β-strand	734-745	12	8
β-strand	767-778	12	8
β-strand	781-788	8	8
β-strand	792	1	8
α-helix	797-798	2
β-strand	799-800	2	13
β-strand	802-804	3	8
β-strand	807	1	8

Chain B: 2 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	44	1	14
β-strand	48-50	3	15
β-strand	71-75	5	16
β-strand	80-85	6	16
β-strand	91-96	6	16
β-strand	111	1	17
β-strand	116-117	2	18
β-strand	121-124	4	18
β-strand	126	1	17
β-strand	130-135	6	18
β-strand	141-146	6	18
β-strand	151	1	19
β-strand	156-158	3	20
β-strand	161-165	5	20
β-strand	166	1	19
β-strand	170-175	6	20
β-strand	183-186	4	20
β-strand	192-194	3	5
α-helix	198-200	3
β-strand	201-203	3	21
β-strand	206-210	5	21
β-strand	215-220	6	21
β-strand	226-231	6	21
β-strand	252-254	3	22
β-strand	257-260	4	22
β-strand	266-271	6	22
β-strand	277-282	6	22
β-strand	290-292	3	23
β-strand	295-299	5	23
β-strand	305-309	5	23
β-strand	315-319	5	23
β-strand	331-333	3	24
β-strand	336-339	4	24
β-strand	345-349	5	24
β-strand	356-361	6	24
β-strand	367	1	25
β-strand	372-374	3	15
β-strand	377-381	5	15
β-strand	382	1	25
β-strand	387-390	4	15
β-strand	392	1	14

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	31-34	4
α-helix	35-38	4
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	48-61	14
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, 5 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	26
α-helix	52-58	7
β-strand	64	1	26
β-strand	72-80	9	26
β-strand	87-95	9	26
β-strand	101-107	7	26

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	809	Escherichia coli K-12	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	400	Escherichia coli K-12	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	344	Escherichia coli K-12	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	245	Escherichia coli K-12	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	121	Escherichia coli K-12	P0A937
Dynobactin A	G	protein	10	Photorhabdus australis	A0A1C0U7H2

Sequence of entity 1 (A), FASTA

>7R1W_1 Outer membrane protein assembly factor BamA (chains A)
MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDIS
NTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVR
VGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQI
NIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI
DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTK
VTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTS
KDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKE
RNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV
DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQ
PQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVT
IPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV
RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT
PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPL
GPLVFSYAQPFKKYDGDKAEQFQFNIGKT

Sequence of entity 2 (B), FASTA

>7R1W_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>7R1W_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>7R1W_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>7R1W_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNKLHHHHH
H

Sequence of entity 6 (G), FASTA

>7R1W_6 Dynobactin A (chains G)
WNSNVHSYRF

Primary citation

Computational identification of a systemic antibiotic for gram-negative bacteria. Miller, R.D., Iinishi, A., Modaresi, S.M. et al. Nat Microbiol (2022) 7:1661-1672. DOI 10.1038/s41564-022-01227-4 · 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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