7A26 | pdb_00007a26

Structure of soluble SmhA crystal form 1 of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.254 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.227 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7A26

This is version 1.1 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, South Yorkshire, UK.

Macromolecule Content 

  • Total Structure Weight: 323.53 kDa 
  • Atom Count: 20,463 
  • Modeled Residue Count: 2,743 
  • Deposited Residue Count: 2,984 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SmhA373Serratia marcescensMutation(s): 0 
Gene Names: BHU62_20100
UniProt
Find proteins for A0A1Q4NVM5 (Serratia marcescens)
Explore A0A1Q4NVM5 
Go to UniProtKB:  A0A1Q4NVM5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Q4NVM5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth BBB]
J [auth CCC]
K [auth CCC]
M [auth FFF]
O [auth GGG]
I [auth BBB],
J [auth CCC],
K [auth CCC],
M [auth FFF],
O [auth GGG],
P [auth HHH]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth CCC],
N [auth FFF],
Q [auth DDD]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A [auth AAA]
B [auth BBB]
C [auth CCC]
D [auth EEE]
E [auth FFF]
A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth EEE],
E [auth FFF],
F [auth GGG],
G [auth HHH],
H [auth DDD]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.254 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.227 (DCC) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.364α = 90
b = 151.364β = 90
c = 133.456γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
CRANKphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary