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	Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 6066, Year 2025
Publish date	Jul 9, 2025
Authors	Daniel R Fox / Kazem Asadollahi / Imogen Samuels / Bradley A Spicer / Ashleigh Kropp / Christopher J Lupton / Kevin Lim / Chunxiao Wang / Hari Venugopal / Marija Dramicanin / Gavin J Knott / Rhys Grinter /
PubMed Abstract	Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron ...Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode transporters capable of extracting the iron-containing cofactor heme directly from host proteins. Pathogenic E. coli and Shigella spp. produce the outer membrane transporter ChuA, which binds host hemoglobin and extracts its heme cofactor, before importing heme into the cell. Heme extraction by ChuA is a dynamic process, with the transporter capable of rapidly extracting heme from hemoglobin in the absence of an external energy source, without forming a stable ChuA-hemoglobin complex. In this work, we utilise a combination of structural modelling, Cryo-EM, X-ray crystallography, mutagenesis, and phenotypic analysis to understand the mechanistic detail of this process. Based on this understanding we utilise artificial intelligence-based protein design to create binders capable of inhibiting E. coli growth by blocking hemoglobin binding to ChuA. By screening a limited number of these designs, we identify several binders that inhibit E. coli growth at low nanomolar concentrations, without experimental optimisation. We determine the structure of a subset of these binders, alone and in complex with ChuA, demonstrating that they closely match the computational design. This work demonstrates the utility of de novo-designed proteins for inhibiting bacterial nutrient uptake and uses a workflow that could be applied to integral membrane proteins in other organisms.
External links	Nat Commun / PubMed:40634285 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.46 - 3.2 Å
Structure data	46916 9dir EMDB-46916, PDB-9dir: Cryo-EM structure of the heme/hemoglobin transporter ChuA, in complex with de novo designed binder G7 Method: EM (single particle) / Resolution: 2.97 Å 46917 9dis EMDB-46917, PDB-9dis: Cryo-EM structure of the heme/hemoglobin transporter ChuA, in complex with de novo designed binder H3 Method: EM (single particle) / Resolution: 2.51 Å PDB-9dhe: The crystal structure on the heme/hemoglobin transporter ChuA, in complex with heme Method: X-RAY DIFFRACTION / Resolution: 3.2 Å PDB-9div: The crystal structure of de novo designed ChuA binding protein C8 Method: X-RAY DIFFRACTION / Resolution: 2.46 Å
Chemicals	ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE ChemComp-HOH: WATER
Source	escherichia coli (E. coli) synthetic construct (others) escherichia coli cft073 (bacteria)
Keywords	TRANSPORT PROTEIN / TonB-dependent transporter / ChuA / Heme / Hemoglobin / Outer-membrane / de novo designed protein / binding protein