Direct localization by cryo-electron microscopy of secondary structural elements in Escherichia coli 23 S rRNA which differ from the corresponding regions in Haloarcula marismortui11Edited by D. E. Draper

2001 ◽  
Vol 307 (5) ◽  
pp. 1341-1349 ◽  
Author(s):  
Rishi Matadeen ◽  
Petr Sergiev ◽  
Andrej Leonov ◽  
Tillmann Pape ◽  
Eli van der Sluis ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Structural Elements ◽  
Cryo Electron Microscopy ◽  
Direct Localization ◽  
Secondary Structural Elements

scholarly journals Structure of the Cytoplasmic Ring of the Xenopus laevis Nuclear Pore Complex

2020 ◽  
Author(s):  
Gaoxingyu Huang ◽  
Yanqing Zhang ◽  
Xuechen Zhu ◽  
Chao Zeng ◽  
Qifan Wang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Xenopus Laevis ◽  
Nuclear Pore Complex ◽  
Single Particle ◽  
Coiled Coil ◽  
Structural Features ◽  
Nuclear Pore ◽  
Structural Elements ◽  
Cryo Electron Microscopy ◽  
Secondary Structural Elements

Nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5-7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighbouring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.

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 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 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 Cryo-EM Reveals the Structural Basis of Microtubule Depolymerization by Kinesin-13s

2017 ◽  
Author(s):  
Matthieu P. M. H. Benoit ◽  
Ana B. Asenjo ◽  
Hernando Sosa
Keyword(s):  
Electron Microscopy ◽  
Conformational Changes ◽  
Distinct Group ◽  
Atomic Resolution ◽  
Structural Basis ◽  
Structural Elements ◽  
Microtubule Depolymerization ◽  
Cryo Electron Microscopy ◽  
Kinesin Superfamily ◽  
Motile Activity

SummaryKinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promotes microtubule depolymerization and lacks motile activity. The molecular mechanism by which the kinesins depolymerize microtubules and are adapted to perform a seemingly very different activity from other kinesins is still unclear. To address this issue we obtained near atomic resolution cryo-electron microscopy (cryo-EM) structures of Drosophila melanogaster kinesin-13 KLP10A constructs bound to curved or straight tubulin in different nucleotide states. The structures show how nucleotide induced conformational changes near the catalytic site are coupled with kinesin-13-specific structural elements to induce tubulin curvature leading to microtubule depolymerization. The data highlight a modular structure that allows similar kinesin core motor-domains to be used for different functions, such as motility or microtubule depolymerization.

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.

scholarly journals Cryo-EM reveals unique structural features of the FhuCDB Escherichia coli ferrichrome importer

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Wenxin Hu ◽  
Hongjin Zheng
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Molecular Basis ◽  
Iron Uptake ◽  
Structural Features ◽  
Biological Processes ◽  
Type Ii ◽  
Functional Studies ◽  
Cryo Electron Microscopy ◽  
Translocation Pathway

AbstractAs one of the most elegant biological processes developed in bacteria, the siderophore-mediated iron uptake demands the action of specific ATP-binding cassette (ABC) importers. Although extensive studies have been done on various ABC importers, the molecular basis of these iron-chelated-siderophore importers are still not fully understood. Here, we report the structure of a ferrichrome importer FhuCDB from Escherichia coli at 3.4 Å resolution determined by cryo electron microscopy. The structure revealed a monomeric membrane subunit of FhuB with a substrate translocation pathway in the middle. In the pathway, there were unique arrangements of residues, especially layers of methionines. Important residues found in the structure were interrogated by mutagenesis and functional studies. Surprisingly, the importer’s ATPase activity was decreased upon FhuD binding, which deviated from the current understanding about bacterial ABC importers. In summary, to the best of our knowledge, these studies not only reveal a new structural twist in the type II ABC importer subfamily, but also provide biological insights in the transport of iron-chelated siderophores.

scholarly journals Assembly principles of a unique cage formed by hexameric and decameric E. coli proteins

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Hélène Malet ◽  
Kaiyin Liu ◽  
Majida El Bakkouri ◽  
Sze Wah Samuel Chan ◽  
Gregory Effantin ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Escherichia Coli ◽  
Lysine Decarboxylase ◽  
Lateral Interactions ◽  
E Coli ◽  
Aaa Atpase ◽  
Cryo Electron Microscopy ◽  
Conformational Rearrangements ◽  
The Individual ◽  
Assembly Principles

A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries–the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI–is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.

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