5ZFU: ExbB/ExbD hexameric complex

Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM). Determined by electron microscopy at 6.7 Å resolution. Released 9 May 2018.

Method: Electron microscopy
Resolution: 6.7 Å
Organism: Escherichia coli K-12
Chains: 9
Atoms: 10,443
Mol. weight: 165.16 kDa
Released: 9 May 2018

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

Secondary structure: helices and β-sheets

5ZFU contains 53 α-helices and 0 β-strands across 9 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	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	130-161	32
α-helix	167-232	66

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	21-51	31
α-helix	53-62	10
α-helix	68-75	8
α-helix	83-97	15
α-helix	105-126	22
α-helix	131-162	32
α-helix	171-232	62

Chain C: 9 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	104-125	22
α-helix	130-152	23
α-helix	155-162	8
α-helix	171-180	10
α-helix	183-231	49

Chain D: 10 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	130-155	26
α-helix	158-161	4
α-helix	167-169	3
α-helix	171-174	4
α-helix	177-228	52

Chain E: 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	167-231	65

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-96	14
α-helix	104-126	23
α-helix	130-139	10
α-helix	145-162	18
α-helix	171-232	62

Chains G, H and I: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-24	4
α-helix	25-35	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbB	A, B, C, D, E, F	protein	244	Escherichia coli K-12	P0ABU7 (AlphaFold model)
22-mer peptide from Biopolymer transport protein ExbD	G, H, I	protein	22	Escherichia coli K-12	P0ABV2 (AlphaFold model)

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

>5ZFU_1 Biopolymer transport protein ExbB (chains A, B, C, D, E, F)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Sequence of entity 2 (G, H, I), FASTA

>5ZFU_2 22-mer peptide from Biopolymer transport protein ExbD (chains G, H, I)
NVTPFIDVMLVLLIIFMVAAPL

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
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
5ZFV 7.1 Å, Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)

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