9GB5 image
Deposition Date 2024-07-29
Release Date 2025-03-26
Last Version Date 2025-04-09
Entry Detail
PDB ID:
9GB5
Keywords:
Title:
Contracted phiCD508 neck
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.27 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp56 - Tail tube protein
Gene (Uniprot):SAMEA1402406_04060, SAMEA3375112_04157
Chain IDs:A, B, C, D, E, F
Chain Length:137
Number of Molecules:6
Biological Source:Clostridioides difficile
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp51 - Neck valve protein
Gene (Uniprot):SAMEA3375112_04162
Chain IDs:G, K, M, O, Q, X
Chain Length:473
Number of Molecules:6
Biological Source:Clostridioides difficile
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp53 - Tail adaptor protein
Gene (Uniprot):SAMEA3375112_04160
Chain IDs:H, L, N, P, R, DA (auth: d)
Chain Length:137
Number of Molecules:6
Biological Source:Clostridioides difficile
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp50 - Portal adaptor protein
Gene (Uniprot):SAMEA3375112_04163
Chain IDs:I, J, S, T, U, V, W, Y, Z, AA (auth: a), BA (auth: b), CA (auth: c)
Chain Length:137
Number of Molecules:12
Biological Source:Clostridioides difficile
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp55 - Tail sheath protein
Gene (Uniprot):SAMEA3375112_04158
Chain IDs:EA (auth: e), FA (auth: f), GA (auth: g), HA (auth: h), IA (auth: i), JA (auth: j)
Chain Length:137
Number of Molecules:6
Biological Source:Clostridioides difficile
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp45 - Portal protein
Chain IDs:KA (auth: k), LA (auth: l), MA (auth: m), NA (auth: n), OA (auth: o), PA (auth: p), QA (auth: q), RA (auth: r), SA (auth: s), TA (auth: t), UA (auth: u), VA (auth: v)
Chain Length:500
Number of Molecules:12
Biological Source:Clostridioides difficile
Ligand Molecules
Primary Citation
Molecular mechanism of bacteriophage contraction structure of an S-layer-penetrating bacteriophage.
Life Sci Alliance 8 ? ? (2025)
PMID: 40139691 DOI: 10.26508/lsa.202403088

Abstact

The molecular details of phage tail contraction and bacterial cell envelope penetration remain poorly understood and are completely unknown for phages infecting bacteria enveloped by proteinaceous S-layers. Here, we reveal the extended and contracted atomic structures of an intact contractile-tailed phage (φCD508) that binds to and penetrates the protective S-layer of the Gram-positive human pathogen Clostridioides difficile The tail is unusually long (225 nm), and it is also notable that the tail contracts less than those studied in related contractile injection systems such as the model phage T4 (∼20% compared with ∼50%). Surprisingly, we find no evidence of auxiliary enzymatic domains that other phages exploit in cell wall penetration, suggesting that sufficient energy is released upon tail contraction to penetrate the S-layer and the thick cell wall without enzymatic activity. Instead, the unusually long tail length, which becomes more flexible upon contraction, likely contributes toward the required free energy release for envelope penetration.

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Disease

Primary Citation of related structures