9CO2: BamA

Crystal structure of BamA in complex with the PTB2 open-state inhibitor (anisotropic data set). Determined by X-ray diffraction at 2.75 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Escherichia coli, synthetic construct
Chains: 8
Atoms: 12,648
Mol. weight: 178.67 kDa
Released: 15 Jan 2025

Explore 9CO2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CO2 contains 32 α-helices and 126 β-strands across 8 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: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	429	1	1
β-strand	440-446	7	1
β-strand	455-462	8	1
β-strand	466-475	10	1
β-strand	484-495	12	1
β-strand	505-518	14	1
β-strand	523-537	15	1
α-helix	539-541	3
β-strand	542	1	2
α-helix	543-551	9
β-strand	560	1	3
β-strand	564-581	18	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	654	1	5
β-strand	662-663	2	6
β-strand	668	1	5
β-strand	671-674	4	2
α-helix	675-676	2
β-strand	677	1	7
β-strand	678	1	3
β-strand	691	1	7
α-helix	692-694	3
β-strand	700-705	6	2
β-strand	708	1	4
β-strand	710-720	11	1
α-helix	730-732	3
β-strand	734-745	12	1
β-strand	767-778	12	1
β-strand	781-792	12	1
β-strand	799-800	2	6
β-strand	802-805	4	1

Chain B: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	429	1	8
β-strand	440-446	7	8
β-strand	455-462	8	8
β-strand	466-475	10	8
β-strand	484-495	12	8
β-strand	505-518	14	8
β-strand	523-537	15	8
α-helix	539-541	3
β-strand	542	1	9
α-helix	543-551	9
β-strand	560	1	10
β-strand	564-581	18	8
β-strand	590-600	11	8
α-helix	601	1
β-strand	608-620	13	8
β-strand	628-640	13	8
α-helix	644-647	4
α-helix	648-650	3
β-strand	652	1	11
β-strand	654	1	12
β-strand	661-663	3	13
β-strand	668	1	12
β-strand	671-674	4	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	700-705	6	9
β-strand	708	1	11
β-strand	710-720	11	8
α-helix	730-732	3
β-strand	734-745	12	8
β-strand	767-778	12	8
β-strand	781-792	12	8
β-strand	799-800	2	13
β-strand	802-805	4	8

Chain C: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	429	1	15
β-strand	440-446	7	15
β-strand	455-462	8	15
β-strand	466-475	10	15
β-strand	484-495	12	15
β-strand	505-518	14	15
β-strand	523-537	15	15
α-helix	539-541	3
β-strand	542	1	16
α-helix	543-551	9
β-strand	560	1	17
β-strand	564-581	18	15
β-strand	590-600	11	15
α-helix	601	1
β-strand	608-620	13	15
β-strand	628-640	13	15
β-strand	641	1	18
α-helix	644-647	4
α-helix	648-650	3
β-strand	652	1	19
β-strand	654	1	20
β-strand	661-663	3	21
β-strand	668	1	20
β-strand	671-674	4	16
α-helix	675-676	2
β-strand	677	1	22
β-strand	678	1	17
β-strand	691	1	22
α-helix	692-694	3
β-strand	700-705	6	16
β-strand	708	1	19
β-strand	710-720	11	15
α-helix	730-732	3
β-strand	734-745	12	15
β-strand	767-778	12	15
β-strand	781-792	12	15
β-strand	799-800	2	21
β-strand	802-805	4	15

Chain D: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	429	1	23
β-strand	440-446	7	23
β-strand	455-462	8	23
β-strand	466-475	10	23
β-strand	484-495	12	23
β-strand	505-518	14	23
β-strand	523-537	15	23
α-helix	539-541	3
β-strand	542	1	24
α-helix	543-551	9
β-strand	560	1	25
β-strand	564-581	18	23
β-strand	590-600	11	23
α-helix	601	1
β-strand	608-620	13	23
β-strand	628-640	13	23
β-strand	641	1	18
α-helix	644-647	4
α-helix	648-650	3
β-strand	652	1	26
β-strand	654	1	27
β-strand	662-663	2	28
β-strand	668	1	27
β-strand	671-674	4	24
α-helix	675-676	2
β-strand	677	1	29
β-strand	678	1	25
β-strand	691	1	29
α-helix	692-694	3
β-strand	700-705	6	24
β-strand	708	1	26
β-strand	710-720	11	23
α-helix	729-732	4
β-strand	734-745	12	23
β-strand	767-778	12	23
β-strand	781-792	12	23
β-strand	799-800	2	28
β-strand	802-805	4	23

Chains E, F, G and I: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	30
β-strand	10-12	3	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A, B, C, D	protein	382	Escherichia coli	P0A940 (AlphaFold model)
PTB2 circular peptide	E, F, G, I	protein	17	synthetic construct

Sequence of entity 1 (A, B, C, D), FASTA

>9CO2_1 Outer membrane protein assembly factor BamA (chains A, B, C, D)
SFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVS
LGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVA
MWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGS
DNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQ
SNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPF
ISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLV
FSYAQPFKKYDGDKAEQFQFNI

Sequence of entity 2 (E, F, G, I), FASTA

>9CO2_2 PTB2 circular peptide (chains E, F, G, I)
XFGTIHKRRFRYWFCGX

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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