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	The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake.
Journal, issue, pages	Nat Commun, Vol. 16, Issue 1, Page 1133, Year 2025
Publish date	Jan 29, 2025
Authors	Imre Gonda / Simona Sorrentino / Laura Galazzo / Nicolas P Lichti / Fabian M Arnold / Ahmad R Mehdipour / Enrica Bordignon / Markus A Seeger /
PubMed Abstract	The mycobacterial ABC transporter IrtAB features an ABC exporter fold, yet it imports iron-charged siderophores called mycobactins. Here, we present extensive cryo-EM analyses and DEER measurements, ...The mycobacterial ABC transporter IrtAB features an ABC exporter fold, yet it imports iron-charged siderophores called mycobactins. Here, we present extensive cryo-EM analyses and DEER measurements, revealing that IrtAB alternates between an inward-facing and an outward-occluded conformation, but does not sample an outward-facing conformation. When IrtAB is locked in its outward-occluded conformation in nanodiscs, mycobactin is bound in the middle of the lipid bilayer at a membrane-facing crevice opening at the heterodimeric interface. Mutations introduced at the crevice abrogate mycobactin import and in corresponding structures, the crevice is collapsed. A conserved triple histidine motif coordinating a zinc ion is present below the mycobactin binding site. Substitution of these histidine residues with alanine results in a decoupled transporter, which hydrolyzes ATP, but lost its capacity to import mycobactins. Our data suggest that IrtAB imports mycobactin via a credit-card mechanism in a transport cycle that is coupled to the presence of zinc.
External links	Nat Commun / PubMed:39880813 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 3.6 Å
Structure data	50820 9fw3 EMDB-50820: Cryo-EM structure of IrtAB 2xEQ mutant in outward-occluded state in complex with mycobactin PDB-9fw3: Cryo-EM structure of IrtAB 2xEQ mutant in outward-occluded state in nanodisc in complex with mycobactin Method: EM (single particle) / Resolution: 2.67 Å 50848 9fxc EMDB-50848, PDB-9fxc: Cryo-EM structure of IrtAB in inward-facing state in nanodisc Method: EM (single particle) / Resolution: 3.6 Å 50977 9g2k EMDB-50977, PDB-9g2k: Cryo-EM structure of IrtAB in outward-occluded state in nanodisc in complex with ADP-vanadate Method: EM (single particle) / Resolution: 3.14 Å 50978 9g2l EMDB-50978, PDB-9g2l: Cryo-EM structure of IrtAB in inward-facing state in LMNG Method: EM (single particle) / Resolution: 3.23 Å 50979 9g2m EMDB-50979, PDB-9g2m: Cryo-EM structure of IrtAB in outward-occluded state in LMNG in complex with ADP-vanadate Method: EM (single particle) / Resolution: 3.23 Å 50980 9g2p EMDB-50980, PDB-9g2p: Cryo-EM structure of IrtAB 2xEQ mutant in outward-occluded state in nanodisc Method: EM (single particle) / Resolution: 2.5 Å 50982 9g2s EMDB-50982, PDB-9g2s: Cryo-EM structure of IrtAB 2xEQ, Q249R_IrtB mutant in LMNG Method: EM (single particle) / Resolution: 2.9 Å 50983 9g2t EMDB-50983, PDB-9g2t: Cryo-EM structure of IrtAB 2xEQ, A256R_IrtB mutant in LMNG Method: EM (single particle) / Resolution: 3.15 Å 50985 9g2v EMDB-50985, PDB-9g2v: Cryo-EM structure of IrtAB in inward-facing state in presence of mycobactin under turnover conditions in LMNG Method: EM (single particle) / Resolution: 3.35 Å 50987 9g2x EMDB-50987, PDB-9g2x: Cryo-EM structure of IrtAB in outward-occluded state in presence of mycobactin under turnover conditions in LMNG Method: EM (single particle) / Resolution: 2.85 Å 50988 9g2y EMDB-50988, PDB-9g2y: Cryo-EM structure of IrtAB in inward-facing state under turnover conditions in LMNG Method: EM (single particle) / Resolution: 3.6 Å 50989 9g2z EMDB-50989: Cryo-EM structure of IrtAB in outward-occluded state under turnover conditions PDB-9g2z: Cryo-EM structure of IrtAB in outward-occluded state under turnover conditions in LMNG Method: EM (single particle) / Resolution: 2.78 Å 50992 9g36 EMDB-50992, PDB-9g36: Cryo-EM structure of IrtAB 3xHtoA mutant in inward-facing state in presence of mycobactin under turnover conditions in LMNG Method: EM (single particle) / Resolution: 3.21 Å 50993 9g37 EMDB-50993, PDB-9g37: Cryo-EM structure of IrtAB 3xHtoA mutant in outward-occluded state in presence of mycobactin under turnover conditions in LMNG Method: EM (single particle) / Resolution: 3.0 Å 51435 9gl3 EMDB-51435, PDB-9gl3: Cryo-EM structure of IrtAB 2xEQ, A256R_IrtB mutant in LMNG Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry PDB-1iry: Solution structure of the hMTH1, a nucleotide pool sanitization enzyme ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-AOV: ADP ORTHOVANADATE / energy-carrying molecule analogueYM ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-HOH: WATER
Source	mycolicibacterium thermoresistibile atcc 19527 (bacteria)
Keywords	MEMBRANE PROTEIN / ABC transporter / type IV ABC importer siderophore / mycobactin / heterodimeric ABC transporter