5D0O: Outer membrane protein assembly factor BamA

BamABCDE complex, outer membrane beta barrel assembly machinery entire complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 5
Atoms: 11,614
Mol. weight: 210.83 kDa
Released: 9 Mar 2016

Explore 5D0O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D0O contains 38 α-helices and 99 β-strands across 5 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: 23 helices, 55 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	56-66	11
α-helix	67-69	3
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	130-142	13
β-strand	150-158	9	3
β-strand	162-170	9	3
α-helix	173-175	3
β-strand	176-183	8	4
α-helix	190-194	5
α-helix	216-232	17
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-275	9	5
α-helix	281-287	7
β-strand	294-295	2	5
α-helix	296	1
α-helix	298-314	17
β-strand	317	1	6
β-strand	321-327	7	5
β-strand	334-342	9	5
β-strand	346	1	6
β-strand	348-355	8	7
α-helix	362-366	5
α-helix	372	1
β-strand	375-376	2	7
α-helix	379-390	12
β-strand	395-404	10	7
α-helix	405	1
β-strand	411-420	10	7
β-strand	424-433	10	8
β-strand	437-446	10	8
β-strand	455-462	8	8
β-strand	466-475	10	8
β-strand	484-485	2	8
β-strand	488-495	8	8
α-helix	496-499	4
β-strand	501	1	9
β-strand	505-518	14	8
β-strand	523-537	15	8
β-strand	542	1	9
α-helix	543-551	9
β-strand	564-579	16	8
β-strand	590-600	11	8
β-strand	602	1	10
β-strand	604	1	10
β-strand	608-620	13	8
β-strand	628-630	3	8
β-strand	632-640	9	8
α-helix	648-650	3
β-strand	652	1	11
β-strand	654	1	12
β-strand	662-663	2	13
α-helix	664	1
β-strand	668	1	12
β-strand	671-674	4	9
α-helix	675-676	2
β-strand	677	1	14
β-strand	691	1	14
α-helix	692-694	3
β-strand	700-705	6	9
β-strand	708	1	11
β-strand	710-720	11	8
β-strand	734-745	12	8
β-strand	767-777	11	8
β-strand	782-792	11	8
α-helix	797-798	2
β-strand	799-800	2	13
β-strand	802-803	2	8
β-strand	805-806	2	8

Chain B: 1 helix, 37 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	15
β-strand	66-67	2	16
β-strand	71-75	5	16
β-strand	80-85	6	16
β-strand	91-96	6	16
β-strand	100-101	2	17
β-strand	105-106	2	17
β-strand	111-117	7	18
β-strand	121-126	6	18
β-strand	130-135	6	18
β-strand	141-146	6	18
β-strand	156-158	3	19
β-strand	161-166	6	19
β-strand	170-175	6	19
β-strand	181-186	6	19
β-strand	192-194	3	4
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	295-297	3	22
β-strand	299	1	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
α-helix	370-371	2
β-strand	372-374	3	15
β-strand	377-379	3	15
β-strand	381	1	15
β-strand	386-390	5	15

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	33-36	4
α-helix	49-51	3

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	32-39	8
α-helix	48-61	14
α-helix	69-82	14
α-helix	85-98	14
α-helix	105-120	16
α-helix	138-153	16
α-helix	160-188	29
α-helix	192-204	13
α-helix	209-224	16
α-helix	228-239	12

Chain E: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	30-31	2
β-strand	32-35	4	24
β-strand	51	1	25
α-helix	52-59	8
β-strand	64	1	24
β-strand	72-80	9	24
β-strand	87-95	9	24
β-strand	100	1	25
β-strand	101-107	7	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	810	Escherichia coli	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	392	Escherichia coli	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	344	Escherichia coli	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	245	Escherichia coli	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	123	Escherichia coli	P0A937

Sequence of entity 1 (A), FASTA

>5D0O_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

>5D0O_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>5D0O_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>5D0O_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>5D0O_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHH
HHH

Primary citation

Structural basis of outer membrane protein insertion by the BAM complex. Gu, Y., Li, H., Dong, H. et al. Nature (2016) 531:47-52. DOI 10.1038/nature17199 · 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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