9HG9: Outer membrane protein assembly factor BamA

Name: PDB 9HG9: BAM-SurA-darobactin complex in the swing-in state
Published: 2025-04-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

BAM-SurA-darobactin complex in the swing-in state. Determined by electron microscopy at 2.88 Å resolution. Released 16 Apr 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Escherichia coli K-12, Photorhabdus
Chains: 7
Atoms: 13,406
Mol. weight: 247.66 kDa
Ligands: MG
Released: 16 Apr 2025

Explore 9HG9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HG9 contains 56 α-helices and 105 β-strands across 7 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: 25 helices, 54 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	1
β-strand	32	1	2
α-helix	39-45	7
α-helix	56-68	13
β-strand	72-77	6	2
β-strand	78-79	2	3
β-strand	84	1	1
β-strand	86-90	5	2
α-helix	91-92	2
β-strand	93-100	8	4
α-helix	107-117	11
β-strand	124	1	4
α-helix	130-144	15
β-strand	151-158	8	4
β-strand	162-169	8	4
α-helix	173-175	3
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
β-strand	267-274	8	6
α-helix	281-285	5
β-strand	294-295	2	6
α-helix	296	1
α-helix	298-314	17
β-strand	321-324	4	6
β-strand	327-329	3	6
β-strand	334-342	9	6
β-strand	348-355	8	7
α-helix	362-366	5
α-helix	372	1
β-strand	375	1	8
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	424-433	10	9
β-strand	439-446	8	9
α-helix	449-451	3
β-strand	455-462	8	9
β-strand	466-474	9	9
β-strand	475	1	10
β-strand	484-485	2	10
β-strand	488-495	8	9
α-helix	497-499	3
β-strand	505-514	10	9
β-strand	515-516	2	10
β-strand	517-518	2	9
β-strand	523-537	15	9
α-helix	539-541	3
β-strand	542	1	11
α-helix	543-551	9
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
α-helix	648-650	3
β-strand	652	1	12
β-strand	654	1	13
β-strand	663	1	14
β-strand	668	1	13
β-strand	671-674	4	11
α-helix	675-676	2
β-strand	677	1	15
β-strand	691	1	15
α-helix	692-694	3
β-strand	700-705	6	11
β-strand	708	1	12
β-strand	710-720	11	9
α-helix	730-732	3
β-strand	733-745	13	9
β-strand	767-778	12	9
β-strand	781-792	12	9
α-helix	797-798	2
β-strand	799	1	14
β-strand	802-806	5	9

Chain B: 4 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	31-37	7
β-strand	44-50	7	16
β-strand	66-67	2	17
β-strand	71-75	5	17
β-strand	80-85	6	17
β-strand	91-96	6	17
β-strand	111	1	18
α-helix	114-115	2
β-strand	116-117	2	19
β-strand	121-125	5	19
β-strand	126	1	18
β-strand	130-135	6	19
β-strand	141-146	6	19
β-strand	151	1	20
β-strand	156-158	3	21
β-strand	161-165	5	21
β-strand	166	1	20
β-strand	170-175	6	21
β-strand	181-186	6	21
β-strand	192-194	3	5
α-helix	198-200	3
β-strand	201-202	2	22
β-strand	206-210	5	22
β-strand	215-220	6	22
β-strand	226-231	6	22
β-strand	252-254	3	23
β-strand	257-261	5	23
β-strand	266-271	6	23
β-strand	277-282	6	23
β-strand	290-292	3	24
β-strand	295-299	5	24
β-strand	305-309	5	24
β-strand	315-319	5	24
β-strand	331-333	3	25
β-strand	336-339	4	25
β-strand	345-350	6	25
β-strand	356-361	6	25
β-strand	367	1	26
α-helix	370-371	2
β-strand	372-374	3	16
β-strand	377-381	5	16
β-strand	382	1	26
β-strand	387-392	6	16

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	31-37	7
α-helix	45-47	3
α-helix	49-53	5
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	48-61	14
α-helix	69-81	13
α-helix	85-98	14
α-helix	103-105	3
α-helix	106-120	15
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-241	14

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
α-helix	29-31	3
β-strand	32-35	4	8
β-strand	51	1	27
α-helix	52-59	8
β-strand	64-65	2	8
β-strand	72-80	9	8
β-strand	87-95	9	8
β-strand	100	1	27
β-strand	101-107	7	8

Chain F: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	3
β-strand	28-32	5	28
β-strand	35-38	4	28
α-helix	39-55	17
α-helix	57-59	3
α-helix	64-87	24
α-helix	93-100	8
α-helix	112-117	6
α-helix	125-148	24
α-helix	154-166	13
α-helix	391-420	30
β-strand	423-425	3	28

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-6	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	790	Escherichia coli K-12	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	381	Escherichia coli K-12	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	320	Escherichia coli K-12	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	226	Escherichia coli K-12	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	102	Escherichia coli K-12	P0A937
Chaperone SurA	F	protein	412	Escherichia coli K-12	P0ABZ6
Darobactin A	G	protein	7	Photorhabdus

Sequence of entity 1 (A), FASTA

>9HG9_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

>9HG9_2 Outer membrane protein assembly factor BamB (chains B)
CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAG
LVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDG
TVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESA
PTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF
ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQ
SDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLL
IQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>9HG9_3 Outer membrane protein assembly factor BamC (chains C)
CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRP
PAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTD
WVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNV
ISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM
KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGH
TLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>9HG9_4 Outer membrane protein assembly factor BamD (chains D)
CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY
YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQH
ARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE
GMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 5 (E), FASTA

>9HG9_5 Outer membrane protein assembly factor BamE (chains E)
CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQ
QPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNKLHHHHHH

Sequence of entity 6 (F), FASTA

>9HG9_6 Chaperone SurA (chains F)
GSHMAPQVVDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIM
DQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEM
IISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAE
SQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIV
GPIRSGVGFHILKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKS
GKTTFAAAAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWH
LIELLDTRNVDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILSN

Sequence of entity 7 (G), FASTA

>9HG9_7 Darobactin A (chains G)
WNXSKSF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Architecture and conformational dynamics of the BAM-SurA holo insertase complex. Lehner, P.A., Degen, M., Jakob, R.P. et al. Sci Adv (2025) 11:eads6094-eads6094. DOI 10.1126/sciadv.ads6094 · 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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