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https://www.readbyqxmd.com/read/28431243/cryo-em-structure-of-the-open-human-ether-%C3%A3-go-go-related-k-channel-herg
#1
Weiwei Wang, Roderick MacKinnon
The human ether-à-go-go-related potassium channel (hERG, Kv11.1) is a voltage-dependent channel known for its role in repolarizing the cardiac action potential. hERG alteration by mutation or pharmacological inhibition produces Long QT syndrome and the lethal cardiac arrhythmia torsade de pointes. We have determined the molecular structure of hERG to 3.8 Å using cryo-electron microscopy. In this structure, the voltage sensors adopt a depolarized conformation, and the pore is open. The central cavity has an atypically small central volume surrounded by four deep hydrophobic pockets, which may explain hERG's unusual sensitivity to many drugs...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28419915/enhanced-imaging-of-lipid-rich-nanoparticles-embedded-in-methylcellulose-films-for-transmission-electron-microscopy-using-mixtures-of-heavy-metals
#2
Jalal Asadi, Sophie Ferguson, Hussain Raja, Christian Hacker, Phedra Marius, Richard Ward, Christos Pliotas, James Naismith, John Lucocq
Synthetic and naturally occurring lipid-rich nanoparticles are of wide ranging importance in biomedicine. They include liposomes, bicelles, nanodiscs, exosomes and virus particles. The quantitative study of these particles requires methods for high-resolution visualization of the whole population. One powerful imaging method is cryo-EM of vitrified samples, but this is technically demanding, requires specialized equipment, provides low contrast and does not reveal all particles present in a population. Another approach is classical negative stain-EM, which is more accessible but is difficult to standardize for larger lipidic structures, which are prone to artifacts of structure collapse and contrast variability...
April 10, 2017: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/28396444/the-cryo-em-structure-of-yjeq-bound-to-the-30s-subunit-suggests-a-fidelity-checkpoint-function-for-this-protein-in-ribosome-assembly
#3
Aida Razi, Alba Guarné, Joaquin Ortega
Recent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-Å resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading...
April 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28393837/cryo-em-structures-of-mers-cov-and-sars-cov-spike-glycoproteins-reveal-the-dynamic-receptor-binding-domains
#4
Yuan Yuan, Duanfang Cao, Yanfang Zhang, Jun Ma, Jianxun Qi, Qihui Wang, Guangwen Lu, Ying Wu, Jinghua Yan, Yi Shi, Xinzheng Zhang, George F Gao
The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD)...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28390173/structure-of-a-aaa-unfoldase-in-the-process-of-unfolding-substrate
#5
Zev A Ripstein, Rui Huang, Rafal Augustyniak, Lewis E Kay, John L Rubinstein
AAA+ unfoldases are thought to unfold substrate through the central pore of their hexameric structures, but how this process occurs is not known. VAT, the Thermoplasma acidophilum homologue of eukaryotic CDC48/p97, works in conjunction with the proteasome to degrade misfolded or damaged proteins. We show that in the presence of ATP, VAT with its regulatory N-terminal domains removed unfolds other VAT complexes as substrate. We captured images of this transient process by electron cryomicroscopy (cryo-EM) to reveal the structure of the substrate-bound intermediate...
April 8, 2017: ELife
https://www.readbyqxmd.com/read/28382301/bayesian-modeling-of-biomolecular-assemblies-with-cryo-em-maps
#6
Michael Habeck
A growing array of experimental techniques allows us to characterize the three-dimensional structure of large biological assemblies at increasingly higher resolution. In addition to X-ray crystallography and nuclear magnetic resonance in solution, new structure determination methods such cryo-electron microscopy (cryo-EM), crosslinking/mass spectrometry and solid-state NMR have emerged. Often it is not sufficient to use a single experimental method, but complementary data need to be collected by using multiple techniques...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28380338/understanding-card-tricks-in-apoptosomes
#7
Li Wang, Qi Qiao, Hao Wu
While earlier studies of Apaf-1 holo-apoptosome architecture revealed the spectacular heptameric wheel-like structure formed by Apaf-1, the central CARD disk responsible for caspase-9 recruitment remained incompletely resolved. In a recent issue of Structure, Su et al. (2017) describe a crystal structure of the complex between Apaf-1 CARD and caspase-9 CARD. Together with two recent cryo-EM structures, this work brings us closer to a full view of the holo-apoptosome.
April 4, 2017: Structure
https://www.readbyqxmd.com/read/28379137/structural-basis-of-protein-translocation-by-the-vps4-vta1-aaa-atpase
#8
Nicole Monroe, Han Han, Peter S Shen, Wesley I Sundquist, Christopher P Hill
Many important cellular membrane fission reactions are driven by ESCRT pathways, which culminate in disassembly of ESCRT-III polymers by the AAA ATPase Vps4. We report a 4.3 Å resolution cryo-EM structure of the active Vps4 hexamer with its cofactor Vta1, ADP•BeFx, and an ESCRT-III substrate peptide. Four Vps4 subunits form a helix whose interfaces are consistent with ATP-binding, is stabilized by Vta1, and binds the substrate peptide. The fifth subunit approximately continues this helix but appears to be dissociating...
April 5, 2017: ELife
https://www.readbyqxmd.com/read/28373698/the-structures-of-a-naturally-empty-cowpea-mosaic-virus-particle-and-its-genome-containing-counterpart-by-cryo-electron-microscopy
#9
Emma L Hesketh, Yulia Meshcheriakova, Rebecca F Thompson, George P Lomonossoff, Neil A Ranson
Cowpea mosaic virus (CPMV) is a picorna-like plant virus. As well as an intrinsic interest in CPMV as a plant pathogen, CPMV is of major interest in biotechnology applications such as nanotechnology. Here, we report high resolution cryo electron microscopy (cryo-EM) maps of wild type CPMV containing RNA-2, and of naturally-formed empty CPMV capsids. The resolution of these structures is sufficient to visualise large amino acids. We have refined an atomic model for each map and identified an essential amino acid involved in genome encapsidation...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28370077/flexible-fitting-to-cryo-em-density-map-using-ensemble-molecular-dynamics-simulations
#10
Osamu Miyashita, Chigusa Kobayashi, Takaharu Mori, Yuji Sugita, Florence Tama
Flexible fitting is a computational algorithm to derive a new conformational model that conforms to low-resolution experimental data by transforming a known structure. A common application is against data from cryo-electron microscopy to obtain conformational models in new functional states. The conventional flexible fitting algorithms cannot derive correct structures in some cases due to the complexity of conformational transitions. In this study, we show the importance of conformational ensemble in the refinement process by performing multiple fittings trials using a variety of different force constants...
April 1, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28368809/a-two-phase-improved-correlation-method-for-automatic-particle-selection-in-cryo-em
#11
Fa Zhang, Yu Chen, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan
Particle selection from cryo-electron microscopy (Cryo-EM) images is very important for high-resolution reconstruction of macromolecular structure. The methods of particle selection can be roughly grouped into two classes, template-matching methods and feature-based methods. In general, template-matching methods usually generate better results than feature-based methods. However, the accuracy of template-matching methods is restricted by the noise and low contrast of Cryo-EM images. Moreover, the processing speed of template-matching methods, restricted by the random orientation of particles, further limits their practical applications...
March 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28368393/structure-of-the-40s-abce1-post-splitting-complex-in-ribosome-recycling-and-translation-initiation
#12
André Heuer, Milan Gerovac, Christian Schmidt, Simon Trowitzsch, Anne Preis, Peter Kötter, Otto Berninghausen, Thomas Becker, Roland Beckmann, Robert Tampé
The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1...
April 3, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28359961/natural-and-artificial-protein-cages-design-structure-and-therapeutic-applications
#13
REVIEW
Jonathan Gardiner Heddle, Soumyananda Chakraborti, Kenji Iwasaki
Advanced electron microscopy techniques have been used to solve many viral capsid structures. The resulting detailed structural knowledge contributes to understanding of the mechanisms of self-assembly, maturation pathways and virion-host cell interactions. It also acts as inspiration for design and production of capsid-like artificial protein cages. Both natural and artificial cages have potential uses in medicine including as vaccines and in drug delivery. For vaccines, virus-like particles formed only from outer virion shells, lacking genetic material, offer the simplest basis for development, while encapsulation of target molecules inside protein cages is potentially more challenging...
March 27, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28352916/a-threonine-turnstile-defines-a-dynamic-amphiphilic-binding-motif-in-the-aaa-atpase-p97-allosteric-binding-site
#14
James C Burnett, Chaemin Lim, Brian D Peyser, Lalith P Samankumara, Marina Kovaliov, Raffaele Colombo, Stacie L Bulfer, Matthew G LaPorte, Ann R Hermone, Connor F McGrath, Michelle R Arkin, Rick Gussio, Donna M Huryn, Peter Wipf
The turnstile motion of two neighboring threonines sets up a dynamic side chain interplay that can accommodate both polar and apolar ligands in a small molecule allosteric protein binding site. A computational model based on SAR data and both X-ray and cryo-EM structures of the AAA ATPase p97 was used to analyze the effects of paired threonines at the inhibitor site. Specifically, the Thr side chain hydroxyl groups form a hydrogen bonding network that readily accommodates small, highly polar ligand substituents...
March 29, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28351611/structural-insights-of-whamm-s-interaction-with-microtubules-by-cryo-em
#15
Tianyang Liu, Anbang Dai, Yong Cao, Rui Zhang, Meng-Qiu Dong, Hong-Wei Wang
WASP homolog associated with actin, membranes, and microtubules (WHAMM) is a vertebrate protein functioning in membrane tubulation for intracellular membrane trafficking and specific organelle formation. Composed of multiple domains, WHAMM can bind to membrane and microtubule (MT) and promote actin polymerization nucleation. Previous work revealed that WHAMM's activity to promote actin nucleation is repressed upon binding to MTs. Here, we discovered that WHAMM interacts with αβ-tubulin through a small peptide motif within its MT-binding domain...
March 25, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28348170/crystal-structure-of-u2-snrnp-sf3b-components-hsh49p-in-complex-with-cus1p-binding-domain
#16
Anne-Marie A M van Roon, Chris Oubridge, Eiji Obayashi, Benedetta Sposito, Andrew James Newman, Bertrand Seraphin, Kiyoshi Nagai
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA binding surface available to bind RNA...
March 27, 2017: RNA
https://www.readbyqxmd.com/read/28344036/focus-the-interface-between-data-collection-and-data-processing-in-cryo-em
#17
Nikhil Biyani, Ricardo D Righetto, Robert McLeod, Daniel Caujolle-Bert, Daniel Castano-Diez, Kenneth N Goldie, Henning Stahlberg
We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions...
March 23, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28342396/high-resolution-cryo-em-the-nuts-and-bolts
#18
REVIEW
Dominika Elmlund, Sarah N Le, Hans Elmlund
Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. Successful high-resolution structure determination by cryo-EM always depends on the quality of the protein sample. While structural heterogeneity remains a key challenge for cryo-EM, it also represents a rare opportunity to study the intrinsic conformational flexibility of macromolecular assemblies...
March 22, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28340353/molecular-structure-of-the-human-cftr-ion-channel
#19
Fangyu Liu, Zhe Zhang, László Csanády, David C Gadsby, Jue Chen
The cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that uniquely functions as an ion channel. Here, we present a 3.9 Å structure of dephosphorylated human CFTR without nucleotides, determined by electron cryomicroscopy (cryo-EM). Close resemblance of this human CFTR structure to zebrafish CFTR under identical conditions reinforces its relevance for understanding CFTR function. The human CFTR structure reveals a previously unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding channel opening...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340349/structure-reveals-mechanisms-of-viral-suppressors-that-intercept-a-crispr-rna-guided-surveillance-complex
#20
Saikat Chowdhury, Joshua Carter, MaryClare F Rollins, Sarah M Golden, Ryan N Jackson, Connor Hoffmann, Lyn'Al Nosaka, Joseph Bondy-Denomy, Karen L Maxwell, Alan R Davidson, Elizabeth R Fischer, Gabriel C Lander, Blake Wiedenheft
Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3...
March 23, 2017: Cell
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