6LYQ: BAM complex

Name: PDB 6LYQ: Structure of the BAM complex
Published: 2021-01-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Structure of the BAM complex. Determined by X-ray diffraction at 3.19 Å resolution. Released 6 Jan 2021.

Method: X-ray diffraction
Resolution: 3.19 Å
Organism: Escherichia coli K-12
Chains: 6
Atoms: 11,463
Mol. weight: 213.31 kDa
Released: 6 Jan 2021

Explore 6LYQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LYQ contains 43 α-helices and 102 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: 22 helices, 59 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29-32	4	2
α-helix	39-43	5
β-strand	53	1	1
α-helix	58-67	10
β-strand	72-80	9	2
β-strand	83-90	8	2
α-helix	91-92	2
β-strand	93-98	6	3
α-helix	107-116	10
β-strand	121	1	4
β-strand	123	1	4
β-strand	124	1	3
α-helix	127-129	3
α-helix	130-144	15
β-strand	154-158	5	3
β-strand	162-166	5	3
α-helix	173-175	3
β-strand	176-183	8	5
α-helix	190-194	5
α-helix	222-231	10
β-strand	239-247	9	5
β-strand	253-261	9	5
α-helix	263-265	3
β-strand	267-276	10	6
α-helix	281-284	4
β-strand	292	1	7
β-strand	294	1	7
β-strand	295	1	6
α-helix	298-314	17
β-strand	317	1	8
β-strand	321-329	9	6
β-strand	334-342	9	6
β-strand	346	1	8
β-strand	348-355	8	9
α-helix	362-366	5
β-strand	375-376	2	9
α-helix	379-390	12
β-strand	395-399	5	9
β-strand	402-404	3	9
α-helix	405	1
β-strand	411-420	10	9
β-strand	424-432	9	10
β-strand	438-446	9	10
α-helix	449-451	3
β-strand	455-462	8	10
β-strand	466-479	14	10
β-strand	483-495	13	10
α-helix	496-498	3
β-strand	501	1	11
β-strand	505-518	14	10
β-strand	523-537	15	10
α-helix	543-549	7
β-strand	560	1	12
β-strand	564-579	16	10
β-strand	590-600	11	10
β-strand	602	1	13
β-strand	604	1	13
β-strand	608-620	13	10
β-strand	628-640	13	10
α-helix	648-650	3
β-strand	652	1	14
β-strand	662-663	2	15
α-helix	664	1
β-strand	671-674	4	11
α-helix	675-676	2
β-strand	677	1	16
β-strand	678	1	12
β-strand	691	1	16
β-strand	700-705	6	11
β-strand	708	1	14
β-strand	710-719	10	10
α-helix	727-730	4
β-strand	736-742	7	10
β-strand	744-745	2	10
β-strand	767-774	8	10
β-strand	777-778	2	17
β-strand	781-782	2	17
β-strand	783-792	10	10
β-strand	799-800	2	15
β-strand	802-806	5	10

Chain B: 3 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	45-51	7	18
β-strand	66-67	2	19
β-strand	71-75	5	19
β-strand	80-85	6	19
β-strand	91-96	6	19
β-strand	111-118	8	20
β-strand	121-126	6	20
β-strand	130-135	6	20
β-strand	141-146	6	20
α-helix	154-155	2
β-strand	156-158	3	21
β-strand	161-165	5	21
β-strand	170-175	6	21
β-strand	181-186	6	21
β-strand	192-193	2	5
α-helix	197-200	4
β-strand	201-203	3	22
β-strand	206-209	4	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	267-271	5	23
β-strand	277-281	5	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
α-helix	327-330	4
β-strand	331-333	3	25
β-strand	336-340	5	25
β-strand	345-350	6	25
β-strand	356-361	6	25
β-strand	372-374	3	18
β-strand	377-381	5	18
β-strand	386-391	6	18

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	40-43	4
α-helix	51-53	3
α-helix	58-60	3
α-helix	77-79	3

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	32-39	8
α-helix	42-45	4
α-helix	48-61	14
α-helix	70-81	12
α-helix	85-98	14
α-helix	105-117	13
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	228-238	11

Chain E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	26
α-helix	40-43	4
β-strand	44	1	27
β-strand	46	1	27
β-strand	51	1	28
α-helix	52-59	8
β-strand	64-65	2	26
β-strand	72-80	9	26
β-strand	87-95	9	26
β-strand	100	1	28
β-strand	101-107	7	26

Chain O: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	280-287	8	10

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	119	Escherichia coli K-12	P0A937
Peptide from Phospholipase A1	O	protein	16	Escherichia coli K-12	P0A921

Sequence of entity 1 (A), FASTA

>6LYQ_1 Outer membrane protein assembly factor BamA (chains A)
MAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDIS
NTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVR
VGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQI
NIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNI
DSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTK
VTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTS
KDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKE
RNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV
DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQ
PQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVT
IPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV
RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT
PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDWSDPSNIRMSAGIALQWMSPL
GPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B), FASTA

>6LYQ_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>6LYQ_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>6LYQ_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>6LYQ_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNHHHHHH

Sequence of entity 6 (O), FASTA

>6LYQ_6 Peptide from Phospholipase A1 (chains O)
FNQTRVGVGVMLNDLF

Primary citation

Structures of the beta-barrel assembly machine recognizing outer membrane protein substrates. Xiao, L., Han, L., Li, B. et al. FASEB J (2021) 35:e21207-e21207. DOI 10.1096/fj.202001443RR · 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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