6LYS: BAM complex

Name: PDB 6LYS: Structure of the BAM complex
Published: 2021-01-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Structure of the BAM complex. Determined by X-ray diffraction at 3.05 Å resolution. Released 13 Jan 2021.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Escherichia coli (strain K12)
Chains: 5
Atoms: 12,196
Mol. weight: 211.48 kDa
Released: 13 Jan 2021

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

Secondary structure: helices and β-sheets

6LYS contains 45 α-helices and 108 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: 25 helices, 58 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	56-67	12
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	130-143	14
β-strand	150-158	9	3
β-strand	162-170	9	3
β-strand	176-183	8	4
α-helix	190-194	5
α-helix	216-231	16
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-273	7	5
α-helix	281-287	7
α-helix	294	1
β-strand	295	1	5
α-helix	296	1
α-helix	298-313	16
β-strand	321-329	9	5
β-strand	334-342	9	5
β-strand	348-355	8	6
α-helix	362-366	5
α-helix	372	1
β-strand	375-376	2	6
α-helix	379-390	12
β-strand	395-404	10	6
β-strand	411-420	10	6
β-strand	424-433	10	7
β-strand	437-446	10	7
β-strand	455-462	8	7
β-strand	466-479	14	7
β-strand	483-485	3	7
β-strand	488-495	8	7
α-helix	496-499	4
β-strand	501	1	8
β-strand	505-518	14	7
β-strand	523-532	10	7
β-strand	535-537	3	7
β-strand	542	1	9
α-helix	543-552	10
β-strand	560	1	10
β-strand	564-566	3	7
β-strand	569-579	11	7
β-strand	590-600	11	7
α-helix	601	1
β-strand	602	1	11
β-strand	604	1	11
β-strand	608-620	13	7
β-strand	628-640	13	7
α-helix	648-650	3
β-strand	652	1	12
β-strand	662-663	2	13
α-helix	664	1
α-helix	670	1
β-strand	671	1	8
α-helix	672	1
β-strand	674	1	9
α-helix	675-676	2
β-strand	677	1	14
β-strand	678	1	10
β-strand	691	1	14
α-helix	692-694	3
β-strand	700	1	9
β-strand	705	1	8
β-strand	708	1	12
β-strand	710-719	10	7
β-strand	720	1	15
α-helix	730-732	3
β-strand	735	1	15
β-strand	736-745	10	7
β-strand	767-778	12	7
β-strand	781-792	12	7
α-helix	797-798	2
β-strand	799-800	2	13
β-strand	802-803	2	7
β-strand	805-806	2	7

Chain B: 2 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	32-36	5
β-strand	46-50	5	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	111-117	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	161-165	5	19
β-strand	170-175	6	19
β-strand	181-186	6	19
β-strand	192	1	4
α-helix	198-200	3
β-strand	201-203	3	20
β-strand	206-209	4	20
β-strand	215-220	6	20
β-strand	226-231	6	20
β-strand	252-254	3	21
β-strand	257-261	5	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	336-340	5	23
β-strand	345	1	24
β-strand	346-350	5	23
β-strand	356-358	3	23
β-strand	361	1	24
β-strand	372-374	3	16
β-strand	377-381	5	16
β-strand	387-390	4	16

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-47	4
α-helix	49-53	5
α-helix	58-61	4
α-helix	74-76	3
β-strand	113-117	5	27
α-helix	128-136	9
α-helix	139-140	2
β-strand	141-145	5	27
β-strand	150-153	4	27
β-strand	156	1	27
β-strand	169-178	10	27
β-strand	181-191	11	27
β-strand	192	1	28
β-strand	197	1	28
α-helix	204-218	15

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	32-43	12
α-helix	48-61	14
α-helix	68-81	14
α-helix	85-98	14
α-helix	105-120	16
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-239	12

Chain E: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	25
β-strand	51	1	26
α-helix	52-59	8
β-strand	64-65	2	25
β-strand	72-80	9	25
β-strand	87-95	9	25
β-strand	100	1	26
β-strand	101-105	5	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	810	Escherichia coli (strain K12)	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	400	Escherichia coli (strain K12)	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	245	Escherichia coli (strain K12)	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	119	Escherichia coli (strain K12)	P0A937 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	344	Escherichia coli (strain K12)	P0A903

Sequence of entity 1 (A), FASTA

>6LYS_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

>6LYS_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (D), FASTA

>6LYS_3 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 4 (E), FASTA

>6LYS_4 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNHHHHHH

Sequence of entity 5 (C), FASTA

>6LYS_5 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

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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