6QGY: E.coli BamA beta-barrel

Name: PDB 6QGY: Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12
Published: 2019-06-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12. Determined by X-ray diffraction at 2.51 Å resolution. Released 26 Jun 2019.

Method: X-ray diffraction
Resolution: 2.51 Å
Organisms: Escherichia coli O157:H7, Lama glama
Chains: 4
Atoms: 8,153
Mol. weight: 122.38 kDa
Ligands: C8E
Released: 26 Jun 2019

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

Secondary structure: helices and β-sheets

6QGY contains 19 α-helices and 84 β-strands across 4 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: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	427-433	7	1
β-strand	437-446	10	1
β-strand	455-462	8	1
β-strand	466-474	9	1
α-helix	476-478	3
β-strand	480	1	2
β-strand	483	1	2
β-strand	484-495	12	1
α-helix	496-499	4
β-strand	501	1	3
β-strand	505-518	14	1
β-strand	523-537	15	1
β-strand	542	1	4
α-helix	543-551	9
β-strand	564-579	16	1
β-strand	590-600	11	1
β-strand	608-620	13	1
β-strand	628-640	13	1
α-helix	648-650	3
β-strand	652	1	5
β-strand	662-663	2	6
β-strand	671	1	3
β-strand	674	1	4
α-helix	675-676	2
β-strand	677	1	7
β-strand	700	1	4
β-strand	705	1	3
β-strand	708	1	5
β-strand	710-720	11	1
α-helix	721-722	2
α-helix	728-732	5
β-strand	733-745	13	1
β-strand	767-778	12	1
β-strand	781-792	12	1
β-strand	799-800	2	6
β-strand	802-809	8	1

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	34-40	7	9
β-strand	47-52	6	9
β-strand	59-61	3	9
β-strand	62	1	7
β-strand	69-73	5	8
β-strand	79-84	6	8
α-helix	89-91	3
β-strand	93-100	8	9
α-helix	108-110	3
β-strand	113-114	2	9
β-strand	118-123	6	9

Chain C: 7 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	427-433	7	10
β-strand	437-446	10	10
β-strand	455-462	8	10
β-strand	466-474	9	10
α-helix	476-478	3
β-strand	480	1	11
β-strand	483	1	11
β-strand	484-495	12	10
α-helix	496-499	4
β-strand	501	1	12
β-strand	505-520	16	10
β-strand	523-537	15	10
β-strand	542	1	13
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	628-640	13	10
α-helix	648-650	3
β-strand	652	1	14
β-strand	654	1	15
β-strand	662-663	2	16
β-strand	668	1	15
β-strand	671	1	12
β-strand	674	1	13
α-helix	675-676	2
β-strand	677	1	17
β-strand	700	1	13
β-strand	705	1	12
β-strand	708	1	14
β-strand	710-720	11	10
α-helix	721-722	2
α-helix	729-732	4
β-strand	733-745	13	10
β-strand	767-778	12	10
β-strand	781-792	12	10
β-strand	799-800	2	16
β-strand	802-806	5	10

Chain D: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	18
β-strand	11-14	4	19
β-strand	19-24	6	18
β-strand	34-40	7	19
β-strand	47-52	6	19
β-strand	59-61	3	19
β-strand	62	1	17
α-helix	63-65	3
β-strand	69-73	5	18
β-strand	79-84	6	18
α-helix	89-91	3
β-strand	93-100	8	19
α-helix	108-110	3
β-strand	113-114	2	19
β-strand	118-123	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A, C	protein	411	Escherichia coli O157:H7	P0A940 (AlphaFold model)
NanoB12	B, D	protein	124	Lama glama

Sequence of entity 1 (A, C), FASTA

>6QGY_1 Outer membrane protein assembly factor BamA (chains A, C)
MGSSHHHHHHSSGENLYFQHMRNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGIN
GTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPI
NEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYN
KLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGD
GLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYESATQDGAKDL
SKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPD
YSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B, D), FASTA

>6QGY_2 NanoB12 (chains B, D)
SQGQLVESGGGMVQAGGSLRLSCAASGRTFNGWTAAWFRQAPGKDREFVAAISRSGDYTY
YTNSVKGRFTISRDSAKNNLYLQMDSLKPEDTAVYYCAAKTGTWATMDRRYDYWGQGTRV
TVSA

Ligands and cofactors

ID	Name	Formula	Copies
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	10

Primary citation

Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach. Kaur, H., Hartmann, J.B., Jakob, R.P. et al. J Biomol NMR (2019) 73:375-384. DOI 10.1007/s10858-019-00250-8 · 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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