8BVQ: E. coli BAM complex

E. coli BAM complex (BamABCDE) bound to darobactin B. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Escherichia coli, Photorhabdus heterorhabditis
Chains: 6
Atoms: 11,875
Mol. weight: 201.28 kDa
Released: 24 May 2023

Explore 8BVQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BVQ contains 41 α-helices and 98 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: 20 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29	1	2
β-strand	32	1	2
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-68	13
β-strand	72-80	9	2
β-strand	83-90	8	2
α-helix	91-92	2
β-strand	93-100	8	3
α-helix	107-116	10
β-strand	124	1	3
α-helix	129-143	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	217-232	16
β-strand	235	1	6
β-strand	239-247	9	5
β-strand	253-261	9	5
β-strand	265	1	6
β-strand	267-276	10	7
α-helix	281-287	7
β-strand	294-295	2	7
α-helix	298-314	17
β-strand	321-329	9	7
β-strand	334-342	9	7
β-strand	348-355	8	8
α-helix	362-366	5
α-helix	372	1
β-strand	375-376	2	8
α-helix	379-392	14
β-strand	395-404	10	8
α-helix	405	1
β-strand	411-420	10	8
β-strand	425-433	9	9
β-strand	437-446	10	9
β-strand	455-462	8	9
β-strand	466-475	10	9
β-strand	484-495	12	9
β-strand	505-520	16	9
β-strand	523-537	15	9
α-helix	539-541	3
β-strand	542	1	10
α-helix	543-552	10
β-strand	564-579	16	9
β-strand	590-600	11	9
α-helix	601	1
β-strand	608-620	13	9
β-strand	628-640	13	9
β-strand	655	1	11
β-strand	663	1	12
β-strand	665	1	11
α-helix	670	1
β-strand	671-674	4	10
β-strand	677	1	13
β-strand	691	1	13
β-strand	700-705	6	10
β-strand	710-720	11	9
β-strand	733-745	13	9
α-helix	750	1
β-strand	767-778	12	9
β-strand	781-789	9	9
α-helix	793-794	2
α-helix	797-798	2
β-strand	799	1	12
β-strand	802-806	5	9

Chain B: 3 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	30-36	7
β-strand	46-50	5	14
β-strand	66-68	3	15
β-strand	71-74	4	15
β-strand	80-85	6	15
β-strand	91-96	6	15
β-strand	100-101	2	16
β-strand	105-106	2	16
β-strand	115	1	17
β-strand	122-124	3	17
β-strand	130	1	18
β-strand	132-134	3	17
β-strand	141-143	3	17
β-strand	146	1	18
α-helix	154-155	2
β-strand	156-158	3	19
β-strand	161-165	5	19
β-strand	170-175	6	19
β-strand	181-186	6	19
β-strand	192-194	3	5
α-helix	198-200	3
β-strand	201-203	3	20
β-strand	206-210	5	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	267-271	5	21
β-strand	277-281	5	21
β-strand	290-292	3	22
β-strand	295-299	5	22
β-strand	305-309	5	22
β-strand	317-319	3	22
β-strand	331-333	3	23
β-strand	336-339	4	23
β-strand	345-350	6	23
β-strand	356-361	6	23
β-strand	372-374	3	14
β-strand	377-381	5	14
β-strand	387-390	4	14

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	34-37	4
α-helix	44-47	4
α-helix	49-51	3
α-helix	58-60	3
α-helix	66-68	3
α-helix	83-86	4

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	32-45	14
α-helix	48-61	14
α-helix	68-82	15
α-helix	85-98	14
α-helix	105-120	16
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	210-224	15
α-helix	229-240	12

Chain E: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	24
β-strand	35	1	8
α-helix	42-45	4
β-strand	51	1	25
α-helix	52-58	7
β-strand	64-65	2	26
β-strand	72-74	3	26
β-strand	79-80	2	24
β-strand	87	1	24
β-strand	90-95	6	26
β-strand	100	1	25
β-strand	101-107	7	26

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	790	Escherichia coli	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	373	Escherichia coli	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	320	Escherichia coli	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	226	Escherichia coli	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	104	Escherichia coli	P0A937
Darobactin-B	G	protein	7	Photorhabdus heterorhabditis

Sequence of entity 1 (A), FASTA

>8BVQ_1 Outer membrane protein assembly factor BamA (chains A)
AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRD
GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDF
YYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLR
DEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNI
TEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP
RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSD
LVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSF
QAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDAD
LSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD
QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVP
IDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQAS
NYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWD
MGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE
QFQFNIGKTW

Sequence of entity 2 (B), FASTA

>8BVQ_2 Outer membrane protein assembly factor BamB (chains B)
CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAG
LVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDG
TVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESA
PTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF
ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQ
SDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLL
IQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>8BVQ_3 Outer membrane protein assembly factor BamC (chains C)
CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRP
PAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTD
WVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNV
ISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM
KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGH
TLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>8BVQ_4 Outer membrane protein assembly factor BamD (chains D)
CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY
YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQH
ARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE
GMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 5 (E), FASTA

>8BVQ_5 Outer membrane protein assembly factor BamE (chains E)
CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQ
QPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHHHHH

Sequence of entity 6 (G), FASTA

>8BVQ_6 Darobactin-B (chains G)
WNXTKRF

Primary citation

Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Haysom, S.F., Machin, J., Whitehouse, J.M. et al. Angew Chem Int Ed Engl (2023) 62:e202218783-e202218783. DOI 10.1002/anie.202218783 · 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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