scholarly journals Mechanistic Insights Revealed by YbtPQ in the Occluded State

2021 ◽  
Author(s):  
Wenxin Hu ◽  
Chance Parkinson ◽  
Hongjin Zheng
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Uropathogenic Escherichia Coli ◽  
Structural Studies ◽  
Binding Domains ◽  
Type Iv ◽  
Cryo Electron Microscopy ◽  
Hinge Points ◽  
Alternating Access ◽  
Shed Light

Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of "alternating access" like those exporters: cycling through conformations of inward-open, occluded, and outward-open. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies in all the major conformations. To shed light on that, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic Escherichia coli in the occluded conformation trapped by ADP-vanadate (ADP.Vi) at 3.1 angstrom resolution determined by cryo electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the "screwdriver" action happening at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.

Escherichia coli 70 S ribosome at 15 Å resolution by cryo-electron microscopy: localization of fmet-tRNAfMet and fitting of L1 protein

1998 ◽  
Vol 280 (1) ◽  
pp. 103-116 ◽  
Author(s):  
Arun Malhotra ◽  
Pawel Penczek ◽  
Rajendra K Agrawal ◽  
Irene S Gabashvili ◽  
Robert A Grassucci ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Cryo Electron Microscopy ◽  
L1 Protein

scholarly journals Direct visualization of Escherichia coli chemotaxis receptor arrays using cryo-electron microscopy

2007 ◽  
Vol 104 (10) ◽  
pp. 3777-3781 ◽  
Author(s):  
P. Zhang ◽  
C. M. Khursigara ◽  
L. M. Hartnell ◽  
S. Subramaniam
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Direct Visualization ◽  
Cryo Electron Microscopy

scholarly journals Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies

2019 ◽  
Vol 17 (1) ◽  
pp. 50-54 ◽  
Author(s):  
Mauricio Toro-Nahuelpan ◽  
Ievgeniia Zagoriy ◽  
Fabrice Senger ◽  
Laurent Blanchoin ◽  
Manuel Théry ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Studies ◽  
Cryo Electron Microscopy

scholarly journals Homologous bd oxidases share the same architecture but differ in mechanism

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexander Theßeling ◽  
Tim Rasmussen ◽  
Sabrina Burschel ◽  
Daniel Wohlwend ◽  
Jan Kägi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Specific Inhibitor ◽  
Protonmotive Force ◽  
Geobacillus Thermodenitrificans ◽  
E Coli ◽  
Cryo Electron Microscopy ◽  
Respiratory Chains

Abstract Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b595 and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism.

scholarly journals Pathogenic siderophore ABC importer YbtPQ adopts a surprising fold of exporter

2020 ◽  
Vol 6 (6) ◽  
pp. eaay7997 ◽  
Author(s):  
Zhiming Wang ◽  
Wenxin Hu ◽  
Hongjin Zheng
Keyword(s):  
Bound States ◽  
Molecular Mechanisms ◽  
Transmembrane Helix ◽  
Human Pathogens ◽  
Binding Domains ◽  
Type Iv ◽  
Cryo Electron Microscopy ◽  
Open Conformation ◽  
Multiple Structures ◽  
First Time

To fight for essential metal ions, human pathogens secrete virulence-associated siderophores and retake the metal-chelated siderophores through a subfamily of adenosine triphosphate (ATP)–binding cassette (ABC) importer, whose molecular mechanisms are completely unknown. We have determined multiple structures of the yersiniabactin importer YbtPQ from uropathogenic Escherichia coli (UPEC) at inward-open conformation in both apo and substrate-bound states by cryo–electron microscopy. YbtPQ does not adopt any known fold of ABC importers but surprisingly adopts the fold of type IV ABC exporters. To our knowledge, it is the first time an exporter fold of ABC importer has been reported. We have also observed two unique features in YbtPQ: unwinding of a transmembrane helix in YbtP upon substrate release and tightly associated nucleotide-binding domains without bound nucleotides. Together, our study suggests that siderophore ABC importers have a distinct transport mechanism and should be classified as a separate subfamily of ABC importers.

scholarly journals The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod

2017 ◽  
Author(s):  
Manuela K. Hospenthal ◽  
Tiago R. D. Costa ◽  
Adam Redzej ◽  
James Lillington ◽  
Gabriel Waksman
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Urinary Tract ◽  
Virulence Factors ◽  
Biomechanical Properties ◽  
Bacterial Attachment ◽  
Host Cells ◽  
Hostile Environment ◽  
Cryo Electron Microscopy

ABSTRACTChaperone-usher pili are long, polymeric protein fibres displayed on the surface of many bacterial pathogens. These critical virulence factors allow bacteria to specifically attach to host cells during infection. The type 1 and P pili of uropathogenicEscherichia coli(UPEC) play important roles during UPEC’s colonisation of the urinary tract, mediating bacterial attachment to the bladder and kidney, respectively. Also, their biomechanical properties that allow them to reversibly uncoil in response to flow-induced forces are critical for UPEC’s ability to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2 Å resolution cryo-electron microscopy (cryo-EM) structure of the type 1 pilus rod, which together with the previous structure of the P pilus rod, enables us to understand the remarkable “spring-like” properties of chaperone-usher pili in more detail.

scholarly journals High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications

2019 ◽  
Author(s):  
Vanja Stojković ◽  
Alexander G. Myasnikov ◽  
Iris D. Young ◽  
Adam Frost ◽  
James S. Fraser ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
High Resolution ◽  
Rna Structure ◽  
Ribosome Biogenesis ◽  
Precise Determination ◽  
23S Rrna ◽  
Modified Nucleotides ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy

ABSTRACTPost-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides’ positions, a task that has previously been accomplished by X-ray crystallography. Here we present a cryo-electron microscopy (cryo-EM) structure of Escherichia coli (E. coli) 50S subunit at an average resolution of 2.2Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for identification of post-transcriptional rRNA modifications using a cryo-EM map. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.

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