› 8et3

Electron Microscopy
3.7Å resolution

Cryo-EM structure of a delivery complex containing the SspB adaptor, an ssrA-tagged substrate, and the AAA+ ClpXP protease

Released:
DOI: 10.2210/pdb8et3/pdb
PDB entry 8et3 coloured by chain, front view.
PDB entry 8et3 coloured by chain, side view.
PDB entry 8et3 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery.
Ghanbarpour A, Fei X, Baker TA, Davis JH, Sauer RT
OpenAccess logo Proc Natl Acad Sci U S A 120 e2219044120 (2023)
PMID: 36730206
Related structures: EMD-28585

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-199612 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
ATP-dependent Clp protease ATP-binding subunit ClpX Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 424 amino acids
Theoretical weight: 46.41 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6H1 (Residues: 1-424; Coverage: 100%)
Gene names: JW0428, b0438, clpX, lopC
Sequence domains:
ATP-dependent Clp protease proteolytic subunit Chains: H, I, J, K, L, M, N
Molecule details ›
Chains: H, I, J, K, L, M, N
Length: 207 amino acids
Theoretical weight: 23.47 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6G7 (Residues: 16-207; Coverage: 93%)
Gene names: JW0427, b0437, clpP, lopP
Sequence domains: Clp protease
Green fluorescent protein Chain: S
Molecule details ›
Chain: S
Length: 273 amino acids
Theoretical weight: 30.86 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P42212 (Residues: 3-238; Coverage: 99%)
Gene name: GFP
Sequence domains: Green fluorescent protein
Stringent starvation protein B Chains: Y, Z
Molecule details ›
Chains: Y, Z
Length: 165 amino acids
Theoretical weight: 18.28 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AFZ3 (Residues: 1-165; Coverage: 100%)
Gene names: JW3197, b3228, sspB
Sequence domains: Stringent starvation protein B

Ligands and Environments

2 bound ligands:
Ligand AGS 4 x AGS
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-28585
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis.
Shu et al. (2024)

1 mention without citation

The SspB adaptor drives structural changes in the AAA+ ClpXP protease during ssrA-tagged substrate delivery.
Ghanbarpour et al. (2023)