6LYR: BAM complex

Name: PDB 6LYR: 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 3.28 Å resolution. Released 6 Jan 2021.

Method: X-ray diffraction
Resolution: 3.28 Å
Organism: Escherichia coli K-12
Chains: 6
Atoms: 11,439
Mol. weight: 212.38 kDa
Released: 6 Jan 2021

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

Secondary structure: helices and β-sheets

6LYR contains 45 α-helices and 99 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: 25 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	28-32	5	2
α-helix	39-43	5
α-helix	49	1
β-strand	53	1	1
α-helix	56-67	12
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	107-115	9
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	151	1	5
β-strand	154-158	5	3
β-strand	162-166	5	3
β-strand	169	1	5
α-helix	173-175	3
β-strand	176-183	8	6
α-helix	190-194	5
α-helix	223-231	9
β-strand	239-247	9	6
β-strand	253-261	9	6
α-helix	262-265	4
β-strand	267-273	7	7
β-strand	276	1	7
α-helix	281-284	4
β-strand	292	1	8
β-strand	294	1	8
β-strand	295	1	7
α-helix	296	1
α-helix	298-314	17
β-strand	321-329	9	7
β-strand	334-342	9	7
β-strand	348-355	8	9
α-helix	362-366	5
α-helix	372	1
β-strand	375-376	2	9
α-helix	379-390	12
β-strand	395-404	10	9
α-helix	405	1
β-strand	411-420	10	9
β-strand	425-431	7	10
β-strand	439-446	8	10
β-strand	455-462	8	10
β-strand	466-475	10	10
β-strand	484-487	4	10
β-strand	491-495	5	10
β-strand	501	1	11
β-strand	505-520	16	10
β-strand	523-537	15	10
β-strand	542	1	11
α-helix	543-551	9
β-strand	564-579	16	10
β-strand	590-600	11	10
β-strand	608-620	13	10
β-strand	628-630	3	10
β-strand	633-640	8	10
α-helix	648-650	3
β-strand	652	1	12
β-strand	662-663	2	13
α-helix	664	1
β-strand	671-674	4	11
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	11
β-strand	708	1	12
β-strand	710-720	11	10
α-helix	730-732	3
β-strand	734-742	9	10
β-strand	744-745	2	10
β-strand	767-778	12	10
β-strand	781-792	12	10
α-helix	797-798	2
β-strand	799-800	2	13
β-strand	802-805	4	10

Chain B: 2 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	45-50	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	111-118	8	17
β-strand	121-126	6	17
β-strand	130-135	6	17
β-strand	141-146	6	17
β-strand	156-158	3	18
β-strand	161-165	5	18
β-strand	171-175	5	18
β-strand	181-185	5	18
β-strand	192	1	6
α-helix	197-200	4
β-strand	201-203	3	19
β-strand	206-209	4	19
β-strand	215-220	6	19
β-strand	228-231	4	19
α-helix	233-235	3
β-strand	252-254	3	20
β-strand	257-261	5	20
β-strand	267-271	5	20
β-strand	277-281	5	20
β-strand	290-292	3	21
β-strand	295-299	5	21
β-strand	305-309	5	21
β-strand	315-319	5	21
β-strand	332-333	2	22
β-strand	336-340	5	22
β-strand	345-350	6	22
β-strand	356-361	6	22
β-strand	367	1	23
β-strand	372-374	3	15
β-strand	377-381	5	15
β-strand	382	1	23
β-strand	387-391	5	15

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	40-43	4
α-helix	45-46	2
α-helix	49-52	4
α-helix	58-62	5
α-helix	77-79	3

Chain D: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	32-42	11
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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	24
α-helix	40-43	4
β-strand	51	1	25
α-helix	52-59	8
β-strand	64-65	2	24
β-strand	72-80	9	24
β-strand	87-94	8	24
β-strand	100	1	25
β-strand	103-107	5	24

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	184-185	2	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 Outer membrane protein A	P	protein	9	Escherichia coli K-12	P0A910

Sequence of entity 1 (A), FASTA

>6LYR_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

>6LYR_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITRWSHPQFEK

Sequence of entity 3 (C), FASTA

>6LYR_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>6LYR_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>6LYR_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNHHHHHH

Sequence of entity 6 (P), FASTA

>6LYR_6 Peptide from Outer membrane protein A (chains P)
NGMLSLGVS

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

Browse structure collections

About this viewer

MolViewer shows 6LYR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.