9HE1: Xenorceptide A2-bound E. coli BAM complex

Name: PDB 9HE1: Structure of the Xenorceptide A2-bound E. coli BAM complex (BamABCDE)
Published: 2025-02-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Structure of the Xenorceptide A2-bound E. coli BAM complex (BamABCDE). Determined by electron microscopy at 3.0 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli K-12, synthetic construct
Chains: 6
Atoms: 11,837
Mol. weight: 213.22 kDa
Released: 26 Feb 2025

Explore 9HE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HE1 contains 36 α-helices and 93 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: 18 helices, 48 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	190-195	6
α-helix	216-232	17
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-276	10	5
α-helix	281-288	8
β-strand	294-295	2	5
α-helix	296	1
α-helix	298-313	16
β-strand	317	1	6
β-strand	320-329	10	5
β-strand	334-343	10	5
β-strand	346	1	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	395-404	10	7
α-helix	405	1
β-strand	411-420	10	7
β-strand	425-433	9	8
β-strand	437-446	10	8
α-helix	449-451	3
β-strand	455-462	8	8
β-strand	466-475	10	8
β-strand	484-495	12	8
β-strand	505-517	13	8
β-strand	523-537	15	8
α-helix	543-552	10
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	9
β-strand	654	1	10
β-strand	656	1	11
β-strand	660	1	11
β-strand	668	1	10
β-strand	671-674	4	12
β-strand	677	1	13
β-strand	691	1	13
β-strand	700-705	6	12
β-strand	708	1	9
β-strand	710-720	11	8
α-helix	727-729	3
β-strand	733-745	13	8
β-strand	767-777	11	8
β-strand	782-789	8	8
β-strand	802-806	5	8

Chain B: 2 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	44-50	7	14
β-strand	66-67	2	15
β-strand	71-75	5	15
β-strand	81-85	5	15
β-strand	91-95	5	15
α-helix	114-115	2
β-strand	116-118	3	16
β-strand	121-124	4	16
β-strand	130-135	6	16
β-strand	141-146	6	16
β-strand	151	1	17
β-strand	156-158	3	18
β-strand	161-165	5	18
β-strand	166	1	17
β-strand	170-175	6	18
β-strand	181-186	6	18
β-strand	192-194	3	4
α-helix	198-200	3
β-strand	201-203	3	19
β-strand	206-210	5	19
β-strand	213	1	20
β-strand	215-219	5	19
β-strand	226-231	6	19
β-strand	246	1	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	315-319	5	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	387-392	6	14

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	33-38	6
α-helix	58-60	3
α-helix	84-85	2

Chain D: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	32-45	14
α-helix	49-61	13
α-helix	68-81	14
α-helix	85-98	14
α-helix	106-120	15
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-212	4
α-helix	215-224	10
α-helix	228-239	12

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	24
α-helix	42-44	3
β-strand	51	1	25
α-helix	52-58	7
β-strand	64-65	2	24
β-strand	72-80	9	24
β-strand	87-95	9	24
β-strand	100	1	25
β-strand	101-107	7	24

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4-11	8	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	810	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
RSAM-modified RiPP, XyeA family	G	protein	12	synthetic construct	A0A1Q4P361

Sequence of entity 1 (A), FASTA

>9HE1_1 Outer membrane protein assembly factor BamA (chains A)
MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDIS
NTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVR
VGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQI
NIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI
DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTK
VTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTS
KDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKE
RNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV
DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQ
PQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVT
IPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV
RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT
PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPL
GPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B), FASTA

>9HE1_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>9HE1_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>9HE1_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>9HE1_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNKLHHHHH
H

Sequence of entity 6 (G), FASTA

>9HE1_6 RSAM-modified RiPP, XyeA family (chains G)
WVNAFARWSKSF

Primary citation

Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA. Modaresi, S.M., Sugiyama, R., Tram, N.D.T. et al. bioRxiv (2024). DOI 10.1101/2024.12.16.628070

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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