8PZV: Outer membrane protein assembly factor BamA

Name: PDB 8PZV: Wait Complex: BAM bound Darobactin-B and Extended SurA
Published: 2024-09-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: membrane protein

Wait Complex: BAM bound Darobactin-B and Extended SurA. Determined by electron microscopy at 2.9 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Escherichia coli, Photorhabdus heterorhabditis
Chains: 7
Atoms: 13,302
Mol. weight: 250.62 kDa
Ligands: MG
Released: 25 Sept 2024

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

Secondary structure: helices and β-sheets

8PZV contains 50 α-helices and 96 β-strands across 7 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: 21 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	1
β-strand	29-30	2	2
α-helix	39-45	7
β-strand	53	1	1
α-helix	56-68	13
β-strand	72-80	9	2
β-strand	83-90	8	2
β-strand	93-100	8	3
α-helix	107-115	9
β-strand	124	1	3
α-helix	130-144	15
β-strand	150-158	9	3
β-strand	162-170	9	3
α-helix	173-175	3
β-strand	176-183	8	4
α-helix	190-194	5
β-strand	213	1	4
α-helix	216-231	16
β-strand	239-247	9	4
β-strand	253-261	9	4
β-strand	267-276	10	5
α-helix	281-287	7
β-strand	294-295	2	5
α-helix	298-313	16
β-strand	320-329	10	5
β-strand	334-343	10	5
β-strand	348-355	8	6
α-helix	362-366	5
α-helix	372	1
β-strand	376	1	6
α-helix	379-392	14
β-strand	395-404	10	6
α-helix	405	1
β-strand	411-420	10	6
β-strand	424-433	10	7
β-strand	437-449	13	7
β-strand	454-462	9	7
β-strand	466-475	10	7
β-strand	484-495	12	7
α-helix	497-499	3
β-strand	501	1	8
β-strand	505-518	14	7
β-strand	523-537	15	7
β-strand	542	1	9
α-helix	543-551	9
β-strand	564-579	16	7
β-strand	590-600	11	7
α-helix	601	1
β-strand	608-620	13	7
β-strand	628-640	13	7
α-helix	648-650	3
β-strand	652	1	10
β-strand	654	1	11
β-strand	656	1	12
β-strand	660	1	12
β-strand	668	1	11
α-helix	670	1
β-strand	671	1	8
α-helix	672	1
β-strand	674	1	9
α-helix	675-676	2
α-helix	692-694	3
β-strand	700	1	9
β-strand	705	1	8
β-strand	708	1	10
β-strand	710-721	12	7
β-strand	733-745	13	7
β-strand	767-778	12	7
β-strand	781-792	12	7
β-strand	802-806	5	7

Chain B: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	31-37	7
β-strand	45-51	7	13
β-strand	71-75	5	14
β-strand	80-85	6	14
β-strand	91-96	6	14
β-strand	99-101	3	15
β-strand	105-107	3	15
β-strand	111-117	7	16
β-strand	121-126	6	16
β-strand	130-135	6	16
β-strand	141-146	6	16
β-strand	156-158	3	17
β-strand	161-165	5	17
β-strand	170-175	6	17
β-strand	181-186	6	17
β-strand	192-194	3	4
α-helix	198-200	3
β-strand	201-202	2	18
β-strand	206-210	5	18
β-strand	215-220	6	18
β-strand	226-231	6	18
α-helix	250-251	2
β-strand	252-254	3	19
β-strand	257-261	5	19
β-strand	267-271	5	19
β-strand	277-281	5	19
β-strand	290-292	3	20
β-strand	295-299	5	20
β-strand	305-309	5	20
β-strand	315-319	5	20
α-helix	327-330	4
β-strand	331-332	2	21
β-strand	336-339	4	21
β-strand	345-350	6	21
β-strand	356-361	6	21
β-strand	367	1	22
α-helix	370-371	2
β-strand	372-374	3	13
β-strand	377-381	5	13
β-strand	382	1	22
β-strand	386-391	6	13

Chain C: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	34-38	5
α-helix	45-46	2
α-helix	49-53	5
α-helix	58-60	3
α-helix	66-68	3
α-helix	84-86	3

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	32-44	13
α-helix	48-61	14
α-helix	68-81	14
α-helix	85-98	14
α-helix	105-119	15
α-helix	138-153	16
α-helix	160-188	29
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-240	13

Chain E: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	23
β-strand	51	1	24
α-helix	52-59	8
β-strand	64-65	2	23
β-strand	72-80	9	23
β-strand	87-95	9	23
β-strand	100	1	24
β-strand	101-107	7	23

Chain F: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	25
β-strand	35-38	4	25
α-helix	39-44	6
α-helix	63-86	24
α-helix	93-105	13
α-helix	111-121	11
α-helix	125-147	23
α-helix	156-162	7
α-helix	396-419	24
β-strand	423-425	3	25

Chain I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Outer membrane protein assembly factor BamA	A	protein	790	Escherichia coli	P0A940 (AlphaFold model)
Outer membrane protein assembly factor BamB	B	protein	373	Escherichia coli	P77774 (AlphaFold model)
Outer membrane protein assembly factor BamC	C	protein	320	Escherichia coli	P0A903 (AlphaFold model)
Outer membrane protein assembly factor BamD	D	protein	226	Escherichia coli	P0AC02 (AlphaFold model)
Outer membrane protein assembly factor BamE	E	protein	104	Escherichia coli	P0A937
Chaperone SurA	F	protein	450	Escherichia coli	P0ABZ6
Darobactin-B	I	protein	7	Photorhabdus heterorhabditis

Sequence of entity 1 (A), FASTA

>8PZV_1 Outer membrane protein assembly factor BamA (chains A)
AEGFVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVCVLRD
GDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDF
YYSVGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLR
DEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNI
TEGDQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYP
RVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSD
LVDQGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSF
QAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDAD
LSDYTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSD
QDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVP
IDDDHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQAS
NYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWD
MGTVWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAE
QFQFNIGKTW

Sequence of entity 2 (B), FASTA

>8PZV_2 Outer membrane protein assembly factor BamB (chains B)
CSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAG
LVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDG
TVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESA
PTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVF
ALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQ
SDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLL
IQAKDGTVYSITR

Sequence of entity 3 (C), FASTA

>8PZV_3 Outer membrane protein assembly factor BamC (chains C)
CSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALDIRP
PAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTLTTD
WVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEMMNV
ISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEKVGM
KVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDPKGH
TLTQSQNDALVAVFQAAFSK

Sequence of entity 4 (D), FASTA

>8PZV_4 Outer membrane protein assembly factor BamD (chains D)
CSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAY
YKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQH
ARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVE
GMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 5 (E), FASTA

>8PZV_5 Outer membrane protein assembly factor BamE (chains E)
CSTLERVVYRPDINQGNYLTANDVSKIRVGMTQQQVAYALGTPLMSDPFGTNTWFYVFRQ
QPGHEGVTQQTLTLTFNSSGVLTNIDNKPALSGNGGHHHHHHHH

Sequence of entity 6 (F), FASTA

>8PZV_6 Chaperone SurA (chains F)
GSSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKSSGENLYFQGAPQVVDCVAAVVNNGVVL
ESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQ
AIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVE
SLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIA
HSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGESK
NISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAAAAKEFSQDPGSANQG
GDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELLDTRNVDKTDAAQKDRAY
RMLMNRKFSEEAASWMQEQRASAYVKILSN

Sequence of entity 7 (I), FASTA

>8PZV_7 Darobactin-B (chains I)
WNXTKRF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Outer membrane protein assembly mediated by BAM-SurA complexes. Fenn, K.L., Horne, J.E., Crossley, J.A. et al. Nat Commun (2024) 15:7612-7612. DOI 10.1038/s41467-024-51358-x · 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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