6TYI: ExbB-ExbD complex in MSP1E3D1 nanodisc

ExbB-ExbD complex in MSP1E3D1 nanodisc. Determined by electron microscopy at 3.3 Å resolution. Released 16 Oct 2019.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Escherichia coli (strain K12)
Chains: 7
Atoms: 9,184
Mol. weight: 170.8 kDa
Ligands: PEV, PGT
Released: 16 Oct 2019

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

Secondary structure: helices and β-sheets

6TYI contains 41 α-helices and 0 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: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	13-18	6
α-helix	22-62	41
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-127	24
α-helix	130-158	29
α-helix	171-174	4
α-helix	177-232	56

Chain B: 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	130-161	32
α-helix	171-232	62

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
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	171-231	61

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-15	4
α-helix	22-62	41
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-127	24
α-helix	130-160	31
α-helix	171-232	62

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	13-15	3
α-helix	24-62	39
α-helix	68-74	7
α-helix	75-77	3
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-161	32
α-helix	171-232	62

Chain Y: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-36	16
α-helix	39-41	3

Chain Z: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	24-35	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbB	A, B, C, D, E	protein	244	Escherichia coli (strain K12)	P0ABU7 (AlphaFold model)
Biopolymer transport protein ExbD	Y, Z	protein	163	Escherichia coli (strain K12)	P0ABV2 (AlphaFold model)

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

>6TYI_1 Biopolymer transport protein ExbB (chains A, B, C, D, E)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Sequence of entity 2 (Y, Z), FASTA

>6TYI_2 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	3
PGT	(1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H79 O10 P	1

Primary citation

Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides information on structure and stoichiometry. Celia, H., Botos, I., Ni, X. et al. Commun Biol (2019) 2:358-358. DOI 10.1038/s42003-019-0604-2 · 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
9DDO 2.8 Å, E. coli TonB-ExbBD TonB bound to ExbB chain C
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
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

About this viewer

MolViewer shows 6TYI directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.