3TGO: E. coli BamCD complex

Crystal structure of the E. coli BamCD complex. Determined by X-ray diffraction at 2.9 Å resolution. Released 28 Sept 2011.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Escherichia coli
Chains: 4
Atoms: 6,466
Mol. weight: 122.24 kDa
Ligands: PO4
Released: 28 Sept 2011

Explore 3TGO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TGO contains 39 α-helices and 17 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: 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	105-125	21
α-helix	138-153	16
α-helix	160-186	27
α-helix	191-204	14
α-helix	209-225	17
α-helix	228-239	12

Chain B: 10 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	105-125	21
α-helix	138-153	16
α-helix	160-186	27
α-helix	191-204	14
α-helix	209-224	16
α-helix	228-239	12

Chain C: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
β-strand	34	1	1
α-helix	40-43	4
α-helix	45-47	3
α-helix	49-53	5
α-helix	59-60	2
α-helix	66-69	4
α-helix	77-79	3
β-strand	81	1	1
α-helix	84-85	2
α-helix	87-89	3
β-strand	96-100	5	2
β-strand	103-108	6	2
α-helix	117-126	10
α-helix	129-130	2
β-strand	131-135	5	2
β-strand	140-147	8	2
β-strand	157-167	11	2
β-strand	172-183	12	2
β-strand	186-187	2	2
α-helix	191-210	20

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
α-helix	40-43	4
α-helix	45-47	3
α-helix	49-53	5
α-helix	77-79	3
β-strand	96-100	5	3
β-strand	103-108	6	3
α-helix	117-127	11
β-strand	131-135	5	3
β-strand	140-143	4	3
β-strand	146-147	2	3
β-strand	157-167	11	3
β-strand	172-183	12	3
β-strand	186-187	2	3
α-helix	191-214	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UPF0169 lipoprotein yfiO	A, B	protein	229	Escherichia coli	P0AC02 (AlphaFold model)
Lipoprotein 34	C, D	protein	323	Escherichia coli	P0A903 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3TGO_1 UPF0169 lipoprotein yfiO (chains A, B)
GSHMSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLI
YAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRD
PQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVN
RVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT

Sequence of entity 2 (C, D), FASTA

>3TGO_2 Lipoprotein 34 (chains C, D)
GSHMSSDSRYKRQVSGDEAYLEAAPLAELHAPAGMILPVTSGDYAIPVTNGSGAVGKALD
IRPPAQPLALVSGARTQFTGDTASLLVENGRGNTLWPQVVSVLQAKNYTITQRDDAGQTL
TTDWVQWNRLDEDEQYRGRYQISVKPQGYQQAVTVKLLNLEQAGKPVADAASMQRYSTEM
MNVISAGLDKSATDAANAAQNRASTTMDVQSAADDTGLPMLVVRGPFNVVWQRLPAALEK
VGMKVTDSTRSQGNMAVTYKPLSDSDWQELGASDPGLASGDYKLQVGDLDNRSSLQFIDP
KGHTLTQSQNDALVAVFQAAFSK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (K, GOL, CL, NA) are not listed.

Primary citation

Crystal structure of the beta-barrel assembly machinery BamCD protein complex. Kim, K.H., Aulakh, S., Paetzel, M. J Biol Chem (2011) 286:39116-39121. DOI 10.1074/jbc.M111.298166 · PubMed

Other PDB entries of the same protein (UniProt P0AC02 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YHC 1.8 Å, Structure of BamD from E. coli
9CNW 2.6 Å, CryoEM structure of the APO-BAM complex in DDM detergent
3Q5M 2.6 Å, Crystal structure of Escherichia coli BamD
9HG6 2.73 Å, BAM-SurA complex in the swing-in state
9HG5 2.82 Å, BAM-SurA complex in the swing-in state with full length BamC resolved
9HG7 2.83 Å, BAM-SurA complex in the swing-out state
9HG9 2.88 Å, BAM-SurA-darobactin complex in the swing-in state
5D0O 2.9 Å, BamABCDE complex, outer membrane beta barrel assembly machinery entire complex
8PZV 2.9 Å, Wait Complex: BAM bound Darobactin-B and Extended SurA
9HG8 2.9 Å, BAM-SurA complex in the swing-out state with BamC resolved
8ADG 3.0 Å, Cryo-EM structure of Darobactin 22 bound BAM complex
9HE1 3.0 Å, Structure of the Xenorceptide A2-bound E. coli BAM complex (BamABCDE)

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