5ZFV: ExbB/ExbD pentameric complex

Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM). Determined by electron microscopy at 7.1 Å resolution. Released 9 May 2018.

Method: Electron microscopy
Resolution: 7.1 Å
Organism: Escherichia coli (strain K12)
Chains: 6
Atoms: 8,446
Mol. weight: 133.99 kDa
Released: 9 May 2018

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

Secondary structure: helices and β-sheets

5ZFV contains 45 α-helices and 0 β-strands across 6 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: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	22-63	42
α-helix	68-74	7
α-helix	83-96	14
α-helix	104-126	23
α-helix	130-161	32
α-helix	172-186	15
α-helix	189-197	9
α-helix	200-228	29

Chain B: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	21-62	42
α-helix	70-76	7
α-helix	83-97	15
α-helix	104-123	20
α-helix	130-158	29
α-helix	167-169	3
α-helix	171-225	55
α-helix	226-230	5

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	21-62	42
α-helix	68-76	9
α-helix	83-97	15
α-helix	104-115	12
α-helix	118-126	9
α-helix	130-131	2
α-helix	132-136	5
α-helix	137-160	24
α-helix	171-225	55
α-helix	226-230	5

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	22-62	41
α-helix	68-74	7
α-helix	76-78	3
α-helix	83-97	15
α-helix	107-125	19
α-helix	128-158	31
α-helix	167-169	3
α-helix	171-230	60

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-62	41
α-helix	68-73	6
α-helix	76-78	3
α-helix	83-97	15
α-helix	104-123	20
α-helix	130-162	33
α-helix	171-228	58

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	25-37	13

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)
22-mer peptide from Biopolymer transport protein ExbD	F	protein	22	Escherichia coli (strain K12)	P0ABV2 (AlphaFold model)

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

>5ZFV_1 Biopolymer transport protein ExbB (chains A, B, C, D, E)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Sequence of entity 2 (F), FASTA

>5ZFV_2 22-mer peptide from Biopolymer transport protein ExbD (chains F)
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
5ZFU 6.7 Å, Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)

Browse structure collections

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