9MGF: Outer membrane protein assembly factor BamA

Name: PDB 9MGF: beta-barrel assembly machine from Escherichia coli in a middle state of substrate assembly
Published: 2025-12-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

beta-barrel assembly machine from Escherichia coli in a middle state of substrate assembly. Determined by electron microscopy at 3.3 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Escherichia coli K-12
Chains: 7
Atoms: 12,080
Mol. weight: 263.82 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9MGF contains 50 α-helices and 101 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: 24 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	28-30	3	2
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-69	14
β-strand	75-78	4	2
β-strand	83-88	6	2
β-strand	94-99	6	3
α-helix	107-117	11
β-strand	123	1	3
α-helix	127-143	17
β-strand	150-158	9	3
β-strand	162-170	9	3
α-helix	174-175	2
β-strand	176-183	8	4
α-helix	190-196	7
α-helix	205-207	3
β-strand	213	1	4
α-helix	216-233	18
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-268	2	5
β-strand	272-274	3	5
α-helix	281-285	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
β-strand	375-376	2	6
α-helix	379-392	14
β-strand	395-404	10	6
α-helix	405	1
β-strand	411-420	10	6
β-strand	425-434	10	7
β-strand	439-449	11	7
β-strand	454-462	9	7
β-strand	466-479	14	7
β-strand	483-494	12	7
β-strand	505-518	14	7
β-strand	523-537	15	7
α-helix	539-541	3
β-strand	542	1	8
α-helix	543-552	10
β-strand	564-580	17	7
β-strand	590-600	11	7
α-helix	601	1
β-strand	608-620	13	7
β-strand	628-640	13	7
α-helix	648-650	3
β-strand	652	1	9
β-strand	656	1	10
β-strand	660	1	10
β-strand	663	1	11
α-helix	670	1
β-strand	671	1	12
α-helix	672	1
β-strand	674	1	8
α-helix	675-676	2
α-helix	680-682	3
α-helix	704	1
β-strand	705	1	12
α-helix	706-707	2
β-strand	708	1	9
β-strand	710-719	10	7
β-strand	733-745	13	7
β-strand	767-778	12	7
β-strand	781-792	12	7
β-strand	799	1	11
β-strand	802-806	5	7

Chain B: 5 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
β-strand	45-51	7	13
β-strand	66-68	3	14
β-strand	71-75	5	14
β-strand	81-85	5	14
β-strand	91-95	5	14
β-strand	111-118	8	15
β-strand	121-126	6	15
β-strand	130-135	6	15
β-strand	141-146	6	15
α-helix	154-155	2
β-strand	156-158	3	16
β-strand	161-165	5	16
β-strand	170-175	6	16
β-strand	181-186	6	16
β-strand	193	1	4
β-strand	201-203	3	17
β-strand	206-209	4	17
β-strand	211	1	18
β-strand	215-220	6	17
β-strand	225-231	7	17
α-helix	241-243	3
β-strand	247	1	18
α-helix	250-251	2
β-strand	252-254	3	19
β-strand	257-260	4	19
β-strand	267-271	5	19
β-strand	277-281	5	19
β-strand	287-292	6	20
β-strand	295-299	5	20
β-strand	305-309	5	20
β-strand	315-319	5	20
β-strand	331-333	3	21
β-strand	336-340	5	21
β-strand	346-350	5	21
β-strand	356-359	4	21
β-strand	367	1	22
α-helix	370-371	2
β-strand	372	1	13
β-strand	379-381	3	13
β-strand	382	1	22
β-strand	386-391	6	13

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	30-32	3
α-helix	34-36	3
α-helix	40-43	4
α-helix	45-47	3
α-helix	52-53	2
α-helix	58-61	4
α-helix	77-79	3
α-helix	84-85	2

Chain D: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-45	14
α-helix	48-61	14
α-helix	68-81	14
α-helix	85-98	14
α-helix	105-120	16
β-strand	124	1	23
β-strand	127	1	23
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	211-224	14
α-helix	228-241	14

Chain E: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	24
α-helix	40-43	4
β-strand	51	1	24
α-helix	52-59	8
β-strand	65	1	24
β-strand	73-80	8	24
β-strand	87-96	10	24
β-strand	100-107	8	24

Chain F: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	611-620	10	7
β-strand	628-637	10	7
β-strand	710-720	11	7
α-helix	727-730	4
β-strand	734-744	11	7
β-strand	766-777	12	7
β-strand	782-788	7	7
β-strand	799-809	11	7

Chain G: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-7	6	7

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	373	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	104	Escherichia coli K-12	P0A937
Outer membrane protein assembly factor BamA	F	protein	568	Escherichia coli K-12	P0A940 (AlphaFold model)
Unknown peptide	G	protein	8	Escherichia coli K-12

Sequence of entity 1 (A), FASTA

>9MGF_1 Outer membrane protein assembly factor BamA (chains A)
AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRD
GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDF
YYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLR
DEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNI
TEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP
RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSD
LVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSF
QAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDAD
LSDYTNKSYGTCVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD
QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVP
IDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQAS
NYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWD
MGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE
QFQFNIGKTW

Sequence of entity 2 (B), FASTA

>9MGF_2 Outer membrane protein assembly factor BamB (chains B)
CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAG
LVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDG
TVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESA
PTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF
ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQ
SDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLL
IQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>9MGF_3 Outer membrane protein assembly factor BamC (chains C)
CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRP
PAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTD
WVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNV
ISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM
KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGH
TLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>9MGF_4 Outer membrane protein assembly factor BamD (chains D)
CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY
YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQH
ARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE
GMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 5 (E), FASTA

>9MGF_5 Outer membrane protein assembly factor BamE (chains E)
CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQ
QPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHHHHH

Sequence of entity 6 (F), FASTA

>9MGF_6 Outer membrane protein assembly factor BamA (chains F)
AWSHPQFEKGGGSGGGSGGSAWSHPQFEKEGFVVKDIHFEGLQRVAVGAALLSMPVRTGD
TVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQ
NLEASGVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEN
TGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDG
VSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQ
VAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTCKVTIP
GSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRG
FQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPT
PFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGP
LVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 7 (G), FASTA

>9MGF_7 Unknown peptide (chains G)
XXXXXXXX

Primary citation

Structures of folding intermediates on BAM show diverse substrates fold by a conserved mechanism. Thomson, B.D., Marquez, M.D., Rawson, S. et al. Proc Natl Acad Sci U S A (2026) 123:e2534936123-e2534936123. DOI 10.1073/pnas.2534936123 · 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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