5ZFP: ExbB/ExbD hexameric complex

Structure of the ExbB/ExbD hexameric complex. Determined by X-ray diffraction at 2.84 Å resolution. Released 9 May 2018.

Method: X-ray diffraction
Resolution: 2.84 Å
Organism: Escherichia coli (strain K12)
Chains: 12
Atoms: 20,653
Mol. weight: 315.75 kDa
Released: 9 May 2018

Explore 5ZFP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZFP contains 97 α-helices and 0 β-strands across 12 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.

Chains A and G: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
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	167-232	66

Chains B, D and F: 8 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	167-169	3
α-helix	171-232	62

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	21-62	42
α-helix	68-74	7
α-helix	75-77	3
α-helix	83-97	15
α-helix	104-125	22
α-helix	130-162	33
α-helix	167-231	65

Chain E: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
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 H: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	21-49	29
α-helix	52-62	11
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	167-169	3
α-helix	171-232	62

Chain I: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-62	41
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 J: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	21-49	29
α-helix	53-62	10
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	167-169	3
α-helix	171-232	62

Chain K: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
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	167-230	64

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbB	A, B, C, D, E, F, G, H, I, J, K, L	protein	244	Escherichia coli (strain K12)	P0ABU7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>5ZFP_1 Biopolymer transport protein ExbB (chains A, B, C, D, E, F, G, H, I, J, K, L)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Primary citation

Hexameric and pentameric complexes of the ExbBD energizer in the Ton system. Maki-Yonekura, S., Matsuoka, R., Yamashita, Y. et al. Elife (2018) 7. DOI 10.7554/eLife.35419 · 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
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)

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