9DDO: E. coli TonB-ExbBD TonB

E. coli TonB-ExbBD TonB bound to ExbB chain C. Determined by electron microscopy at 2.8 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Escherichia coli
Chains: 8
Atoms: 9,252
Mol. weight: 197.82 kDa
Ligands: PEV
Released: 9 Jul 2025

Explore 9DDO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DDO contains 41 α-helices and 0 β-strands across 8 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, 0 β-strands

Element	Residues	Length
α-helix	14-17	4
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-161	32
α-helix	167-229	63

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-96	14
α-helix	104-126	23
α-helix	130-162	33
α-helix	167-231	65

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	68-74	7
α-helix	75-77	3
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-162	33
α-helix	167-231	65

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-162	33
α-helix	171-230	60

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-96	14
α-helix	104-126	23
α-helix	130-162	33
α-helix	167-170	4
α-helix	171-232	62

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-31	21

Chain Y: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-37	17
α-helix	38-40	3

Chain Z: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	22-36	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbB	A, B, C, D, E	protein	244	Escherichia coli	P0ABU7 (AlphaFold model)
Protein TonB	F	protein	261	Escherichia coli	P02929 (AlphaFold model)
Biopolymer transport protein ExbD	Y, Z	protein	163	Escherichia coli	P0ABV2 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>9DDO_1 Biopolymer transport protein ExbB (chains A, B, C, D, E)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Sequence of entity 2 (F), FASTA

>9DDO_2 Protein TonB (chains F)
MTLDLPRRFPWPTLLSVCIHGAVVAGLLYTSVHQVIELPAPAQPISVTMVTPADLEPPQA
VQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESR
PASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQVKVKF
DVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGTTEIQG
GGSENLYFQGGSAWSHPQFEK

Sequence of entity 3 (Y, Z), FASTA

>9DDO_3 Biopolymer transport protein ExbD (chains Y, Z)
MAMHLNENLDDNGEMHDINVTPFIDVMLVLLIIFMVAAPLATVDVKVNLPASTSTPQPRP
EKPVYLSVKADNSMFIGNDPVTDETMITALNALTEGKKDTTIFFRADKTVDYETLMKVMD
TLHQAGYLKIGLVGEETAKAKENLYFQGNAGSGHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PEV	(1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl…	C39 H78 N O8 P	2

Primary citation

Cryo-EM structures of the E. coli Ton and Tol motor complexes. Celia, H., Botos, I., Ghirlando, R. et al. Nat Commun (2025) 16:5506-5506. DOI 10.1038/s41467-025-61286-z · PubMed

Other PDB entries of the same protein (UniProt P0ABU7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5SV0 2.6 Å, Structure of the ExbB/ExbD complex from E. coli at pH 7.0
5ZFP 2.84 Å, Structure of the ExbB/ExbD hexameric complex
9DDP 3.16 Å, E. coli TonB-ExbBD TonB bound to ExbB chain E
9DDQ 3.19 Å, E. coli TonB-ExbBD TonB bound to ExbB chain A
6TYI 3.3 Å, ExbB-ExbD complex in MSP1E3D1 nanodisc
5SV1 3.5 Å, Structure of the ExbB/ExbD complex from E. coli at pH 4.5
5ZFU 6.7 Å, Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
5ZFV 7.1 Å, Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)

Browse structure collections

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