9CS1: E. coli BamA beta-barrel

E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2. Determined by X-ray diffraction at 2.15 Å resolution. Released 16 Apr 2025.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Escherichia coli, synthetic construct, Photorhabdus khanii
Chains: 3
Atoms: 3,145
Mol. weight: 46.85 kDa
Ligands: 4NE
Released: 16 Apr 2025

Explore 9CS1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CS1 contains 9 α-helices and 26 β-strands across 2 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: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	424-433	10	1
β-strand	437-446	10	1
α-helix	449-451	3
β-strand	455-462	8	1
β-strand	466-475	10	1
β-strand	484-495	12	1
α-helix	497-499	3
β-strand	501	1	2
β-strand	505-518	14	1
β-strand	523-537	15	1
α-helix	539-541	3
β-strand	542	1	3
α-helix	543-551	9
β-strand	564-579	16	1
β-strand	590-600	11	1
α-helix	601	1
β-strand	608-620	13	1
β-strand	628-640	13	1
α-helix	644-647	4
α-helix	648-650	3
β-strand	652	1	4
β-strand	662-663	2	5
β-strand	671	1	2
β-strand	674	1	3
β-strand	705	1	2
β-strand	708	1	4
β-strand	710-720	11	1
α-helix	721-722	2
β-strand	733-745	13	1
β-strand	767-778	12	1
β-strand	781-792	12	1
α-helix	797-798	2
β-strand	799-800	2	5
β-strand	802-806	5	1

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-6	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	390	Escherichia coli	P0A940 (AlphaFold model)
Cyclic peptide CP2	C	protein	17	synthetic construct
Darobactin A	D	protein	7	Photorhabdus khanii

Sequence of entity 1 (A), FASTA

>9CS1_1 Outer membrane protein assembly factor BamA (chains A)
MNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTV
DGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQ
PQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVT
IPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTV
RGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFIT
PTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPL
GPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (C), FASTA

>9CS1_2 Cyclic peptide CP2 (chains C)
XFSGRWXWPSRSVGCGX

Sequence of entity 3 (D), FASTA

>9CS1_3 Darobactin A (chains D)
WNXSKSF

Ligands and cofactors

ID	Name	Formula	Copies
4NE	tetrabutylphosphonium	C16 H36 P	2

Primary citation

Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition. Walker, M.E., Zhu, W., Peterson, J.H. et al. Nat Commun (2025) 16:3395-3395. DOI 10.1038/s41467-025-58086-w · 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
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
6QGY 2.51 Å, Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12

Browse structure collections

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