7NRF: E.coli BamA beta-barrel

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2). Determined by X-ray diffraction at 2.2 Å resolution. Released 21 Apr 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Escherichia coli O157:H7, synthetic construct
Chains: 2
Atoms: 3,227
Mol. weight: 49.47 kDa
Ligands: C8E, MG
Released: 21 Apr 2021

Explore 7NRF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NRF contains 8 α-helices and 25 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: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	425-433	9	1
β-strand	437-446	10	1
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
β-strand	542	1	2
α-helix	543-552	10
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	648-650	3
β-strand	652	1	3
β-strand	662-663	2	4
α-helix	664	1
β-strand	671-674	4	2
α-helix	675-677	3
β-strand	700-705	6	2
β-strand	708	1	3
β-strand	710-720	11	1
α-helix	721-722	2
α-helix	727-729	3
β-strand	733-745	13	1
β-strand	767-778	12	1
β-strand	781-792	12	1
β-strand	799-800	2	4
β-strand	802-806	5	1

Chain B: 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	411	Escherichia coli O157:H7	P0A940 (AlphaFold model)
Darobactin	B	protein	7	synthetic construct

Sequence of entity 1 (A), FASTA

>7NRF_1 Outer membrane protein assembly factor BamA (chains A)
MGSSHHHHHHSSGENLYFQHMRNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGIN
GTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPI
NEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYN
KLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGD
GLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYESATQDGAKDL
SKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPD
YSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B), FASTA

>7NRF_2 Darobactin (chains B)
WNXSKSF

Ligands and cofactors

ID	Name	Formula	Copies
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	8
MG	Magnesium ion	Mg	1

Primary citation

The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase. Kaur, H., Jakob, R.P., Marzinek, J.K. et al. Nature (2021) 593:125-129. DOI 10.1038/s41586-021-03455-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
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
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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