6GRJ | pdb_00006grj

Structure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.

• PDB DOI: https://doi.org/10.2210/pdb6GRJ/pdb

• Classification: TOXIN
• Organism(s): Aeromonas hydrophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-06-11 Released: 2019-07-03 
• Deposition Author(s): Churchill-Angus, A.M., Wilson, J.S., Baker, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.239 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Identification and structural analysis of the tripartite alpha-pore forming toxin of Aeromonas hydrophila.

Wilson, J.S., Churchill-Angus, A.M., Davies, S.P., Sedelnikova, S.E., Tzokov, S.B., Rafferty, J.B., Bullough, P.A., Bisson, C., Baker, P.J.

(2019) Nat Commun 10: 2900-2900

• PubMed: 31263098 
• DOI: https://doi.org/10.1038/s41467-019-10777-x
• Primary Citation Related Structures: 
  6GRJ, 6GRK, 6H2D, 6H2E, 6H2F, 6R1J


• PubMed Abstract: 
  

  The alpha helical CytolysinA family of pore forming toxins (α-PFT) contains single, two, and three component members. Structures of the single component Eschericia coli ClyA and the two component Yersinia enterolytica YaxAB show both undergo conformational changes from soluble to pore forms, and oligomerization to produce the active pore. Here we identify tripartite α-PFTs in pathogenic Gram negative bacteria, including Aeromonas hydrophila (AhlABC). We show that the AhlABC toxin requires all three components for maximal cell lysis. We present structures of pore components which describe a bi-fold hinge mechanism for soluble to pore transition in AhlB and a contrasting tetrameric assembly employed by soluble AhlC to hide their hydrophobic membrane associated residues. We propose a model of pore assembly where the AhlC tetramer dissociates, binds a single membrane leaflet, recruits AhlB promoting soluble to pore transition, prior to AhlA binding to form the active hydrophilic lined pore.

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Organizational Affiliation: 
• Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK.
School of Biomedical Sciences, Faculty of Biological Sciences and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
ISMB, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.
Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, South Yorkshire, S10 2TN, 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: 393.48 kDa 
• Atom Count: 24,385 
• Modeled Residue Count: 3,285 
• Deposited Residue Count: 3,670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AhlB	A [auth G], B [auth J], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth H], J [auth I]	367	Aeromonas hydrophila	Mutation(s): 1  Gene Names: A9R12_16795
UniProt
Find proteins for A0A454GEH4 (Aeromonas hydrophila) Explore A0A454GEH4  Go to UniProtKB:  A0A454GEH4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	AA [auth C], AB [auth H], BA [auth C], BB [auth H], GB [auth I], K [auth G], L [auth G], M [auth G], NA [auth E], OA [auth E], R [auth J], S [auth J], UA [auth F], V [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	N [auth G], PA [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	CA [auth C], CB [auth H], DA [auth C], DB [auth H], EA [auth C], EB [auth H], FA [auth C], GA [auth C], HB [auth I], IB [auth I], JB [auth I], KA [auth D], KB [auth I], LA [auth D], O [auth G], P [auth G], Q [auth G], QA [auth E], RA [auth E], T [auth J], VA [auth F], W [auth A], WA [auth F], X [auth B], XA [auth F], Y [auth B], YA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	FB [auth H], HA [auth C], IA [auth C], JA [auth C], MA [auth D], SA [auth E], TA [auth E], U [auth J], Z [auth B], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth G], B [auth J], C [auth A], D [auth B], E [auth C], F [auth D], G [auth E], H [auth F], I [auth H], J [auth I]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.239 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 363.644	α = 90
b = 116.526	β = 118.01
c = 217.409	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Churchill-Angus, A.M., Wilson, J.S., Baker, P.J.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Database references
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary