8ADG: Darobactin 22 bound BAM complex

Cryo-EM structure of Darobactin 22 bound BAM complex. Determined by electron microscopy at 3.0 Å resolution. Released 11 Jan 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli, Escherichia coli K-12, synthetic construct
Chains: 6
Atoms: 11,808
Mol. weight: 214.43 kDa
Released: 11 Jan 2023

Explore 8ADG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ADG contains 43 α-helices and 97 β-strands across 6 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: 24 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29-32	4	2
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	107-117	11
β-strand	124	1	3
α-helix	125-126	2
α-helix	130-144	15
β-strand	150-158	9	3
β-strand	162-170	9	3
β-strand	176-183	8	4
α-helix	190-193	4
α-helix	194-196	3
α-helix	216-231	16
β-strand	235	1	5
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	265	1	5
β-strand	267-270	4	6
β-strand	273-276	4	6
α-helix	281-285	5
α-helix	286-288	3
α-helix	294	1
β-strand	295	1	6
α-helix	296	1
α-helix	299-313	15
β-strand	320-329	10	6
β-strand	334-343	10	6
β-strand	348-355	8	7
α-helix	362-366	5
β-strand	376	1	7
α-helix	379-392	14
β-strand	395-404	10	7
β-strand	411-420	10	7
α-helix	421-422	2
β-strand	424-433	10	8
β-strand	439-446	8	8
α-helix	449-451	3
β-strand	455-462	8	8
β-strand	466-475	10	8
β-strand	484-495	12	8
α-helix	497-499	3
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	564-579	16	8
β-strand	590-600	11	8
α-helix	601	1
β-strand	608-620	13	8
β-strand	628-640	13	8
β-strand	652	1	10
β-strand	654	1	11
β-strand	656	1	12
β-strand	660	1	12
β-strand	663	1	13
β-strand	668	1	11
β-strand	671	1	14
β-strand	674	1	9
α-helix	692-694	3
β-strand	700	1	9
β-strand	705	1	14
β-strand	708	1	10
β-strand	710-720	11	8
α-helix	730-732	3
β-strand	733-745	13	8
β-strand	767-778	12	8
β-strand	781-792	12	8
β-strand	799	1	13
β-strand	802-806	5	8

Chain B: 2 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	31-37	7
β-strand	45-50	6	15
β-strand	66-67	2	16
β-strand	71-75	5	16
β-strand	80-85	6	16
β-strand	91-96	6	16
β-strand	111-117	7	17
β-strand	122-126	5	17
β-strand	130-134	5	17
β-strand	141-146	6	17
β-strand	151	1	18
β-strand	156-158	3	19
β-strand	161-165	5	19
β-strand	166	1	18
β-strand	170-175	6	19
β-strand	183-186	4	19
β-strand	192-194	3	4
α-helix	198-200	3
β-strand	201-202	2	20
β-strand	206-210	5	20
β-strand	215-220	6	20
β-strand	226-231	6	20
β-strand	252-254	3	21
β-strand	257-260	4	21
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	317-319	3	22
β-strand	327	1	23
β-strand	331-333	3	24
β-strand	336-339	4	24
β-strand	341	1	23
β-strand	345-349	5	24
β-strand	356-361	6	24
β-strand	372-374	3	15
β-strand	377-381	5	15
β-strand	387-391	5	15

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	31-38	8
α-helix	45-47	3
α-helix	58-60	3
α-helix	84-85	2

Chain D: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	32-45	14
α-helix	48-61	14
α-helix	68-81	14
α-helix	85-98	14
α-helix	103-105	3
α-helix	106-120	15
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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	25
α-helix	43-45	3
β-strand	51	1	26
α-helix	52-58	7
β-strand	64-65	2	25
β-strand	72-80	9	25
β-strand	87-94	8	25
β-strand	100	1	26
β-strand	103-107	5	25

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-5	3	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	813	Escherichia coli	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	405	Escherichia coli	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	347	Escherichia coli	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	248	Escherichia coli K-12	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	124	Escherichia coli	P0A937
Darobactin 22	F	protein	7	synthetic construct

Sequence of entity 1 (A), FASTA

>8ADG_1 Outer membrane protein assembly factor BamA (chains A)
MGSMAMKKLLIASLLFSSATVYGAEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDE
DISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEAS
GVRVGESLDRTTIADIEKGLEDFYYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEI
QQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYAR
FNIDSTQVSLTPDKKGIYVTVNITEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYN
GTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGN
DTSKDAVLRREMRQMEGAWLGSDLVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYK
VKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPY
FTVDGVSLGGRLFYNDFQADDADLSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLS
NMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTG
KVTIPGSDNEYYKVTLDTATYVPIDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGS
STVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLE
FITPTPFISDKYANSVRTSFFWDMGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWM
SPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKTW

Sequence of entity 2 (B), FASTA

>8ADG_2 Outer membrane protein assembly factor BamB (chains B)
MGSMQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIG
NFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTV
SGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEA
DGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATG
STEIDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIY
LVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFV
AQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITRKLWSHPQFEK

Sequence of entity 3 (C), FASTA

>8ADG_3 Outer membrane protein assembly factor BamC (chains C)
MGSMAYSVQKSRLAKVAGVSLVLLLAACSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMI
LPVTSGDYAIPVTNGSGAVGKALDIRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLW
PQVVSVLQAKNYTITQRDDAGQTLTTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVK
LLNLEQAGKPVADAASMQRYSTEMMNVISAGLDKSATDAANAAQNRASTTMDVQSAADDT
GLPMLVVRGPFNVVWQRLPAALEKVGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPG
LASGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>8ADG_4 Outer membrane protein assembly factor BamD (chains D)
MGSMTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEA
LDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNM
ALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKY
EYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKI
IAANSSNT

Sequence of entity 5 (E), FASTA

>8ADG_5 Outer membrane protein assembly factor BamE (chains E)
MGSMRCKTLTAAAAVLLMLTAGCSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAY
ALGTPLMSDPFGTNTWFYVFRQQPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNKLHH
HHHH

Sequence of entity 6 (F), FASTA

>8ADG_6 Darobactin 22 (chains F)
WNXTKRW

Primary citation

Darobactins Exhibiting Superior Antibiotic Activity by Cryo-EM Structure Guided Biosynthetic Engineering. Seyfert, C.E., Porten, C., Yuan, B. et al. Angew Chem Int Ed Engl (2023) 62:e202214094-e202214094. DOI 10.1002/anie.202214094 · 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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