8P9R: Periplasmic domain of ExbD from E. coli

Structure of the periplasmic domain of ExbD from E. coli in complex with TonB. Determined by X-ray diffraction at 1.52 Å resolution. Released 6 Sept 2023.

Method: X-ray diffraction
Resolution: 1.52 Å
Organism: Escherichia coli
Chains: 3
Atoms: 1,291
Mol. weight: 20.62 kDa
Released: 6 Sept 2023

Explore 8P9R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P9R contains 4 α-helices and 14 β-strands across 3 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: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	64-68	5	1
β-strand	74-76	3	1
β-strand	79-81	3	1
α-helix	86-94	9
β-strand	102-106	5	1
β-strand	111	1	2
α-helix	112-124	13
β-strand	130-133	4	1

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	64-68	5	3
β-strand	74-76	3	3
β-strand	79-81	3	3
α-helix	86-94	9
β-strand	102-106	5	3
β-strand	111	1	2
α-helix	112-124	13
β-strand	130-132	3	3

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	45-46	2	3
β-strand	48-50	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbD	A, B	protein	82	Escherichia coli	P0ABV2 (AlphaFold model)
Protein TonB	C	protein	23	Escherichia coli	P02929 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8P9R_1 Biopolymer transport protein ExbD (chains A, B)
SEKPVYLSVKADNSMFIGNDPVTDETMITALNALTEGKKDTTIFFRADKTVDYETLMKVM
DTLHQAGYLKIGLVGEETAKAK

Sequence of entity 2 (C), FASTA

>8P9R_2 Protein TonB (chains C)
KKAQPISVTMVTPADLEPPQAKK

Primary citation

Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Zinke, M., Lejeune, M., Mechaly, A. et al. Nat Commun (2024) 15:331-331. DOI 10.1038/s41467-023-44606-z · PubMed

Other PDB entries of the same protein (UniProt P0ABV2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VGC 1.42 Å, Complex of ExbD with D-box peptide: Orthorhombic form
8VGD 1.42 Å, Complex of ExbD with D-box peptide: Tetragonal form
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)
2PFU NMR structure determination of the periplasmic domain of ExbD from E.coli

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