5SV1: ExbB/ExbD complex from E. coli at pH 4.5

Structure of the ExbB/ExbD complex from E. coli at pH 4.5. Determined by X-ray diffraction at 3.5 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Escherichia coli DH1
Chains: 12
Atoms: 16,946
Mol. weight: 278.24 kDa
Ligands: HG
Released: 28 Sept 2016

Explore 5SV1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SV1 contains 75 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.

Chain A: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-161	32
α-helix	172-230	59

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	69-74	6
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-159	30
α-helix	167-169	3
α-helix	171-230	60

Chains C and H: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	22-62	41
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-162	33
α-helix	167-230	64

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-62	41
α-helix	68-74	7
α-helix	84-97	14
α-helix	104-126	23
α-helix	130-159	30
α-helix	167-169	3
α-helix	171-230	60

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	13-16	4
α-helix	22-62	41
α-helix	68-74	7
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-162	33
α-helix	170-230	61

Chain F: 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	130-160	31
α-helix	171-232	62

Chain G: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	21-62	42
α-helix	69-74	6
α-helix	76-78	3
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-159	30
α-helix	171-230	60

Chain I: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-62	41
α-helix	69-74	6
α-helix	83-97	15
α-helix	104-126	23
α-helix	130-159	30
α-helix	167-169	3
α-helix	171-230	60

3 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)
Biopolymer transport protein ExbD	Y, Z	protein	58	Escherichia coli DH1	P0ABV2 (AlphaFold model)

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

>5SV1_1 Biopolymer transport protein ExbB (chains A, B, C, D, E, F, G, H, I, J)
MGNNLMQTDLSVWGMYQHADIVVKCVMIGLILASVVTWAIFFSKSVEFFNQKRRLKREQQ
LLAEARSLNQANDIAADFGSKSLSLHLLNEAQNELELSEGSDDNEGIKERTSFRLERRVA
AVGRQMGRGNGYLATIGAISPFVGLFGTVWGIMNSFIGIAQTQTTNLAVVAPGIAEALLA
TAIGLVAAIPAVVIYNVFARQIGGFKAMLGDVAAQVLLLQSRDLDLEASAAAHPVRVAQK
LRAG

Sequence of entity 2 (Y, Z), FASTA

>5SV1_2 Biopolymer transport protein ExbD (chains Y, Z)
MAMHLNENLDDNGEMHDINVTPFIDVMLVLLIIFMVAAPLATVDVKVNLGGGENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	10

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:

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
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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