Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Conformational changes during pore formation by the perforin-related protein pleurotolysin.
Journal, issue, pages	PLoS Biol, Vol. 13, Issue 2, Page e1002049, Year 2015
Publish date	Feb 5, 2015
Authors	Natalya Lukoyanova / Stephanie C Kondos / Irene Farabella / Ruby H P Law / Cyril F Reboul / Tom T Caradoc-Davies / Bradley A Spicer / Oded Kleifeld / Daouda A K Traore / Susan M Ekkel / Ilia Voskoboinik / Joseph A Trapani / Tamas Hatfaludi / Katherine Oliver / Eileen M Hotze / Rodney K Tweten / James C Whisstock / Maya Topf / Helen R Saibil / Michelle A Dunstone /
PubMed Abstract	Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into ...Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally and mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure of the two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures of both components (the lipid binding PlyA protein and the pore-forming MACPF component PlyB). These data reveal a 13-fold pore 80 Å in diameter and 100 Å in height, with each subunit comprised of a PlyB molecule atop a membrane bound dimer of PlyA. The resolution of the EM map, together with biophysical and computational experiments, allowed confident assignment of subdomains in a MACPF pore assembly. The major conformational changes in PlyB are a ∼70° opening of the bent and distorted central β-sheet of the MACPF domain, accompanied by extrusion and refolding of two α-helical regions into transmembrane β-hairpins (TMH1 and TMH2). We determined the structures of three different disulphide bond-trapped prepore intermediates. Analysis of these data by molecular modelling and flexible fitting allows us to generate a potential trajectory of β-sheet unbending. The results suggest that MACPF conformational change is triggered through disruption of the interface between a conserved helix-turn-helix motif and the top of TMH2. Following their release we propose that the transmembrane regions assemble into β-hairpins via top down zippering of backbone hydrogen bonds to form the membrane-inserted β-barrel. The intermediate structures of the MACPF domain during refolding into the β-barrel pore establish a structural paradigm for the transition from soluble monomer to pore, which may be conserved across the whole superfamily. The TMH2 region is critical for the release of both TMH clusters, suggesting why this region is targeted by endogenous inhibitors of MACPF function.
External links	PLoS Biol / PubMed:25654333 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.85 - 17.0 Å
Structure data	2793 4v2t EMDB-2793, PDB-4v2t: Membrane embedded pleurotolysin pore with 13 fold symmetry Method: EM (single particle) / Resolution: 11.0 Å 2794 4v3a EMDB-2794, PDB-4v3a: Membrane bound pleurotolysin prepore (TMH1 lock) trapped with engineered disulphide cross-link Method: EM (single particle) / Resolution: 15.0 Å 2795 4v3m EMDB-2795, PDB-4v3m: Membrane bound pleurotolysin prepore (TMH2 helix lock) trapped with engineered disulphide cross-link Method: EM (single particle) / Resolution: 17.0 Å 2796 4v3n EMDB-2796, PDB-4v3n: Membrane bound pleurotolysin prepore (TMH2 strand lock) trapped with engineered disulphide cross-link Method: EM (single particle) / Resolution: 14.0 Å PDB-4oeb: Structure of membrane binding protein pleurotolysin A from Pleurotus ostreatus Method: X-RAY DIFFRACTION / Resolution: 1.85 Å PDB-4oej: Structure of membrane binding protein pleurotolysin B from Pleurotus ostreatus Method: X-RAY DIFFRACTION / Resolution: 2.2 Å PDB-4ov8: Crystal Structure of the TMH1-lock mutant of the mature form of pleurotolysin B Method: X-RAY DIFFRACTION / Resolution: 2.15 Å
Chemicals	ChemComp-SO4: SULFATE ION / Sulfate ChemComp-HOH: WATER / Water ChemComp-ACT: ACETATE ION / Acetate ChemComp-GOL: GLYCEROL / Glycerol ChemComp-CL: Unknown entry / Chloride
Source	pleurotus ostreatus (oyster mushroom)
Keywords	MEMBRANE BINDING PROTEIN / beta-sandwich fold / pleurotolysin B / MACPF domain / Pore formation / pleurotolysin A / TOXIN / TMH1-lock / pore-forming protein / Pleurtolysin A component / TRANSPORT PROTEIN / MACPF/CDC SUPERFAMILY / PORE-FORMING PROTEINS