7A0G | pdb_00007a0g

Structure of the SmhB pore of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.

• PDB DOI: https://doi.org/10.2210/pdb7A0G/pdb

• Classification: TOXIN
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-08-08 Released: 2021-03-31 
• Deposition Author(s): Churchill-Angus, A.M., Baker, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.98 Å
• R-Value Free: 
  0.335 (Depositor), 0.391 (DCC) 
• R-Value Work: 
  0.334 (Depositor), 0.350 (DCC) 

Starting Model: experimental

Literature

Characterisation of a tripartite alpha-pore forming toxin from Serratia marcescens

Churchill-Angus, A.M., Schofield, T.H.B., Marlow, T.R., Sedelnikova, S.E., Wilson, J.S., Rafferty, J.B., Baker, P.J.

(2021) Sci Rep 11: 6447

• PubMed: 33742033 
• DOI: https://doi.org/10.1038/s41598-021-85726-0
• Primary Citation Related Structures: 
  6ZZ5, 6ZZH, 7A0G, 7A26, 7A27


• PubMed Abstract: 
  

  Tripartite members of the ClyA family of α-PFTs have recently been identified in a number of pathogenic Gram-negative bacteria, including the human pathogen Serratia marcescens. Structures of a Gram-negative A component and a tripartite α-PFT complete pore are unknown and a mechanism for pore formation is still uncertain. Here we characterise the tripartite SmhABC toxin from S. marcescens and propose a mechanism of pore assembly. We present the structure of soluble SmhA, as well as the soluble and pore forms of SmhB. We show that the β-tongue soluble structure is well conserved in the family and propose two conserved latches between the head and tail domains that are broken on the soluble to pore conformational change. Using the structures of individual components, sequence analysis and docking predictions we illustrate how the A, B and C protomers would assemble on the membrane to produce a complete tripartite α-PFT pore.

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Organizational Affiliation: 
• Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, South Yorkshire, UK.
Current address: Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, South Yorkshire, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 393.77 kDa 
• Atom Count: 15,780 
• Modeled Residue Count: 3,228 
• Deposited Residue Count: 3,660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SmhB	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF], G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ]	366	Serratia marcescens	Mutation(s): 0  Gene Names: BHU62_20105 Membrane Entity: Yes
UniProt
Find proteins for A0A1Q4NVM7 (Serratia marcescens) Explore A0A1Q4NVM7  Go to UniProtKB:  A0A1Q4NVM7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.98 Å
• R-Value Free:  0.335 (Depositor), 0.391 (DCC) 
• R-Value Work:  0.334 (Depositor), 0.350 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.481	α = 90
b = 118.062	β = 109.438
c = 209.532	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Churchill-Angus, A.M., Baker, P.J.

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description