5SV0: ExbB/ExbD complex from E. coli at pH 7.0

Structure of the ExbB/ExbD complex from E. coli at pH 7.0. Determined by X-ray diffraction at 2.6 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Escherichia coli DH1
Chains: 10
Atoms: 16,861
Mol. weight: 264.19 kDa
Ligands: CA
Released: 28 Sept 2016

Explore 5SV0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SV0 contains 70 α-helices and 0 β-strands across 10 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	12-16	5
α-helix	21-62	42
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-127	24
α-helix	130-161	32
α-helix	171-232	62

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
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	167-169	3
α-helix	171-232	62

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	21-63	43
α-helix	68-74	7
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	22-62	41
α-helix	68-75	8
α-helix	83-97	15
α-helix	104-127	24
α-helix	130-160	31
α-helix	167-169	3
α-helix	171-232	62

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	21-62	42
α-helix	68-75	8
α-helix	83-97	15
α-helix	104-127	24
α-helix	130-159	30
α-helix	171-230	60

Chain F: 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	130-159	30
α-helix	170-232	63

Chain G: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-16	5
α-helix	21-62	42
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-162	33
α-helix	171-232	62

Chain H: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-17	7
α-helix	21-63	43
α-helix	69-75	7
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

2 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	protein	244	Escherichia coli DH1	P0ABU7 (AlphaFold model)

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

>5SV0_1 Biopolymer transport protein ExbB (chains A, B, C, D, E, F, G, H, I, J)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (EPE) are not listed.

Primary citation

Structural insight into the role of the Ton complex in energy transduction. Celia, H., Noinaj, N., Zakharov, S.D. et al. Nature (2016) 538:60-65. DOI 10.1038/nature19757 · PubMed

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

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

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