› 8v43

Electron Microscopy
6.1Å resolution

CryoEM Structure of Diffocin - postcontracted - Baseplate - final state

Released:
DOI: 10.2210/pdb8v43/pdb
PDB entry 8v43 coloured by chain, front view.
PDB entry 8v43 coloured by chain, side view.
PDB entry 8v43 coloured by chain, top view.
Source organism: Clostridioides difficile
Primary publication:
Atomic structures of a bacteriocin targeting Gram-positive bacteria.
Cai X, He Y, Yu I, Imani A, Scholl D, Miller JF, Zhou ZH
Nat Commun 15 7057 (2024)
PMID: 39152109
Related structures: EMD-42964

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 42-mer (preferred)
PDBe Complex ID:
PDB-CPX-268502 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Baseplate protein J-like domain-containing protein Chains: B, F, K, O, Q, R, Z, e, m, n, o, v
Molecule details ›
Chains: B, F, K, O, Q, R, Z, e, m, n, o, v
Length: 350 amino acids
Theoretical weight: 39.6 KDa
Source organism: Clostridioides difficile
Expression system: Bacillus subtilis
UniProt:
  • Canonical: A0A1X9JZB1 (Residues: 1-350; Coverage: 100%)
Gene names: KRM00_000621, SAMEA3375112_00273, rtbJ
Sequence domains: Baseplate J-like protein
Base plate protein Chains: A, E, L, M, N, Y
Molecule details ›
Chains: A, E, L, M, N, Y
Length: 232 amino acids
Theoretical weight: 26.47 KDa
Source organism: Clostridioides difficile
Expression system: Bacillus subtilis
UniProt:
  • Canonical: A0A1X9JZH3 (Residues: 1-232; Coverage: 100%)
Gene names: KRM00_000622, SAMEA3375112_00274, rtbK
Sequence domains: Bacteriophage Mu-like, Gp48
Putative phage XkdS-like protein Chains: J, d, i, j, k, l
Molecule details ›
Chains: J, d, i, j, k, l
Length: 142 amino acids
Theoretical weight: 16.55 KDa
Source organism: Clostridioides difficile
Expression system: Bacillus subtilis
UniProt:
  • Canonical: A0A069AE46 (Residues: 1-142; Coverage: 100%)
Gene names: BN1095_340097, BN1096_560288, BN1097_540291, KRM00_000620, SAMEA3375112_00272
Sequence domains: Protein of unknown function (DUF2634)
Phage tail sheath protein Chains: C, D, G, H, I, P, S, T, U, V, W, X, a, b, c, f, g, h
Molecule details ›
Chains: C, D, G, H, I, P, S, T, U, V, W, X, a, b, c, f, g, h
Length: 354 amino acids
Theoretical weight: 39.27 KDa
Source organism: Clostridioides difficile
Expression system: Bacillus subtilis
UniProt:
  • Canonical: A0A9Q7ZU73 (Residues: 1-354; Coverage: 100%)
Gene names: KRM00_000612, SAMEA1402406_02043, SAMEA3375112_00264
Sequence domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.1Å
Relevant EMDB volumes: EMD-42964
Expression system: Bacillus subtilis

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