9CNW: APO-BAM complex in DDM detergent

CryoEM structure of the APO-BAM complex in DDM detergent. Determined by electron microscopy at 2.6 Å resolution. Released 25 Dec 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 5
Atoms: 11,647
Mol. weight: 210.83 kDa
Released: 25 Dec 2024

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

Secondary structure: helices and β-sheets

9CNW contains 51 α-helices and 96 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, 50 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-68	13
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	107-116	10
β-strand	124	1	3
α-helix	127-129	3
α-helix	130-144	15
β-strand	150-157	8	3
β-strand	162-170	9	3
α-helix	173-175	3
β-strand	176-183	8	4
α-helix	190-194	5
β-strand	213	1	4
α-helix	216-232	17
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-276	10	5
α-helix	281-287	7
α-helix	294	1
β-strand	295	1	5
α-helix	296	1
α-helix	298-314	17
β-strand	321-329	9	5
β-strand	334-342	9	5
α-helix	345-347	3
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
α-helix	405	1
β-strand	411-420	10	6
β-strand	424-426	3	7
β-strand	429-430	2	7
β-strand	440-449	10	7
β-strand	454-462	9	7
β-strand	466-475	10	7
β-strand	484-495	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	543-551	9
β-strand	564-579	16	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	654	1	10
β-strand	656	1	11
β-strand	660	1	11
β-strand	663	1	12
β-strand	668	1	10
β-strand	671-674	4	8
β-strand	677	1	13
α-helix	678-679	2
β-strand	691	1	13
α-helix	692-694	3
β-strand	700-705	6	8
β-strand	708	1	9
β-strand	710-720	11	7
α-helix	727-732	6
β-strand	733-745	13	7
β-strand	767-778	12	7
β-strand	781-792	12	7
β-strand	799	1	12
β-strand	802-806	5	7

Chain B: 4 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	31-36	6
β-strand	46-50	5	14
β-strand	66-68	3	15
β-strand	71-75	5	15
β-strand	80-85	6	15
β-strand	91-96	6	15
β-strand	111	1	16
β-strand	116-118	3	17
β-strand	121-125	5	17
β-strand	126	1	16
β-strand	130-135	6	17
β-strand	141-146	6	17
α-helix	154-155	2
β-strand	156-158	3	18
β-strand	161-165	5	18
β-strand	170-175	6	18
β-strand	181-186	6	18
β-strand	192-194	3	4
α-helix	198-200	3
β-strand	201-203	3	19
β-strand	206-210	5	19
β-strand	215-220	6	19
β-strand	225-231	7	19
β-strand	248	1	20
β-strand	252-254	3	21
β-strand	257-261	5	21
β-strand	262	1	20
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	327	1	23
β-strand	331-333	3	24
β-strand	336-340	5	24
β-strand	341	1	23
β-strand	345-350	6	24
β-strand	356-361	6	24
α-helix	370-371	2
β-strand	372-374	3	14
β-strand	377-381	5	14
β-strand	387-390	4	14

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	35	1
α-helix	39-43	5
α-helix	44-47	4
α-helix	49-53	5
α-helix	58-62	5
α-helix	77-79	3
α-helix	84-86	3

Chain D: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	32-45	14
α-helix	48-61	14
α-helix	68-82	15
α-helix	85-98	14
α-helix	105-119	15
α-helix	123-127	5
α-helix	132-134	3
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-241	14

Chain E: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	25
α-helix	40-44	5
β-strand	51	1	26
α-helix	52-59	8
β-strand	64-65	2	25
β-strand	72-80	9	25
α-helix	85-86	2
β-strand	87-95	9	25
β-strand	100	1	26
β-strand	101-107	7	25

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

>9CNW_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

>9CNW_2 Outer membrane protein assembly factor BamB (chains B)
MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFY
SNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGG
HVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGA
VKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTE
IDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVD
QNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQ
KVDSSGFQTEPVAADGKLLIQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>9CNW_3 Outer membrane protein assembly factor BamC (chains C)
MAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPV
TSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQV
VSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLN
LEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLP
MLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLAS
GDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>9CNW_4 Outer membrane protein assembly factor BamD (chains D)
MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDN
RYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALD
DSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYS
VAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAA
NSSNT

Sequence of entity 5 (E), FASTA

>9CNW_5 Outer membrane protein assembly factor BamE (chains E)
MRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALG
TPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHH
HHH

Primary citation

The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Sun, D., Storek, K.M., Tegunov, D. et al. Nat Commun (2024) 15:8718-8718. DOI 10.1038/s41467-024-52512-1 · 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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