8VGC: Biopolymer transport protein ExbD

Name: PDB 8VGC: Complex of ExbD with D-box peptide: Orthorhombic form
Published: 2024-02-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transport protein

Complex of ExbD with D-box peptide: Orthorhombic form. Determined by X-ray diffraction at 1.42 Å resolution. Released 14 Feb 2024.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Escherichia coli
Chains: 3
Atoms: 1,346
Mol. weight: 19.55 kDa
Released: 14 Feb 2024

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

Secondary structure: helices and β-sheets

8VGC contains 5 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: 3 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
α-helix	101	1
β-strand	102-106	5	3
β-strand	111	1	2
α-helix	112-124	13
β-strand	130-133	4	3

Chain P: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	57-59	3	3
β-strand	60-62	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport protein ExbD	A, B	protein	83	Escherichia coli	P0ABV2 (AlphaFold model)
Gln-pro-ile-ser-val-thr-met-val-thr-pro	P	protein	10	Escherichia coli	P02929 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VGC_1 Biopolymer transport protein ExbD (chains A, B)
RPEKPVYLSVKADNSMFIGNDPVTDETMITALNALTEGKKDTTIFFRADKTVDYETLMKV
MDTLHQAGYLKIGLVGEETAKAK

Sequence of entity 2 (P), FASTA

>8VGC_2 GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THR-PRO (chains P)
QPISVTMVTP

Primary citation

Discovery and structural characterization of the D-box, a conserved TonB motif that couples an inner-membrane motor to outer-membrane transport. Loll, P.J., Grasty, K.C., Shultis, D.D. et al. J Biol Chem (2024) 300:105723-105723. DOI 10.1016/j.jbc.2024.105723 · PubMed

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

8VGD 1.42 Å, Complex of ExbD with D-box peptide: Tetragonal form
8P9R 1.52 Å, Structure of the periplasmic domain of ExbD from E. coli in complex with TonB
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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