In situ electron microscopy characterization of intracellular ion pools in mineral forming microalgae
Publication date: Available online 22 January 2020Source: Journal of Structural BiologyAuthor(s): Yuval Kadan, Lior Aram, Eyal Shimoni, Smadar Levin-Zaidman, Shilo Rosenwasser, Assaf GalAbstractThe formation of coccoliths, intricate calcium carbonate scales that cover the cells of unicellular marine microalgae, is a highly regulated biological process. For decades, scientists have tried to elucidate the cellular, chemical, and structural mechanisms that control the precise mineralogy and shape of the inorganic crystals. Transmission electron microscopy was pivotal in characterizing some of the organelles that orchestrate t...
Source: Journal of Structural Biology - January 23, 2020 Category: Biology Source Type: research

A structural entropy index to analyse local conformations in Intrinsically Disordered Proteins
In this study, we used an ensemble of disordered proteins (or regions) and, we applied a structural alphabet to analyse their local conformation. This structural alphabet, namely Protein Blocks, had been efficiently used to highlight rigid local domains within flexible regions and so discriminates deformability and mobility concepts. Using an entropy index derived from this structural alphabet, we underlined its interest to measure these local dynamics, and to quantify, for the first time, continuum states from rigidity to flexibility and finally disorder. We also highlight non-disordered regions in the ensemble of disorde...
Source: Journal of Structural Biology - January 23, 2020 Category: Biology Source Type: research

Higher-Order Oligomerization of a Chimeric αβγ Bifunctional Diterpene Synthase with Prenyltransferase and Class II Cyclase Activities is Concentration-Dependent
Publication date: Available online 21 January 2020Source: Journal of Structural BiologyAuthor(s): Trey A. Ronnebaum, Kushol Gupta, David W. ChristiansonAbstractThe unusual diterpene (C20) synthase copalyl diphosphate synthase from Penicillium verruculosum (PvCPS) is the first bifunctional terpene synthase identified with both prenyltransferase and class II cyclase activities in a single polypeptide chain with αβγ domain architecture. The C-terminal prenyltransferase αdomain generates geranylgeranyl diphosphate which is then cyclized to form copalyl diphosphate at the N-terminal βγ domain i...
Source: Journal of Structural Biology - January 21, 2020 Category: Biology Source Type: research

A cryo-tomography-based volumetric model of the actin core of mouse vestibular hair cell stereocilia lacking plastin 1
Publication date: Available online 18 January 2020Source: Journal of Structural BiologyAuthor(s): Junha Song, Roma Patterson, Zoltan Metlagel, Jocelyn F. Krey, Samantha Hao, Linshanshan Wang, Brian Ng, Salim Sazzed, Julio Kovacs, Willy Wriggers, Jing He, Peter G. Barr-Gillespie, Manfred AuerAbstractElectron cryo-tomography allows for high-resolution imaging of stereocilia in their native state. Because their actin filaments have a higher degree of order, we imaged stereocilia from mice lacking the actin crosslinker plastin 1 (PLS1). We found that while stereocilia actin filaments run 13 nm apart in parallel for long d...
Source: Journal of Structural Biology - January 20, 2020 Category: Biology Source Type: research

Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues
Publication date: Available online 18 January 2020Source: Journal of Structural BiologyAuthor(s): Claudia Minici, Laura Mosca, Concetta Paola Ilisso, Giovanna Cacciapuoti, Marina Porcelli, Massimo DeganoAbstractMethionine adenosyltransferases catalyse the biosynthesis of S-adenosylmethionine, the primary methyl group donor in biochemical reactions, through the condensation of methionine and ATP. Here, we report the structural analysis of the Pyrococcus furiosus methionine adenosyltransferase (PfMAT) captured in the unliganded, substrate- and product-bound states. The conformational changes taking place during the enzymatic...
Source: Journal of Structural Biology - January 20, 2020 Category: Biology Source Type: research

Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin
This study provides a structural basis for understanding the molecular mechanism of actomyosin system.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 18, 2020 Category: Biology Source Type: research

Clearing, immunofluorescence, and confocal microscopy for the three-dimensional imaging of murine testes and study of testis biology
Publication date: Available online 10 January 2020Source: Journal of Structural BiologyAuthor(s): Jason A. Kaufman, Monica J. Castro, Saul A. Ruiz, Garilyn M. Jentarra, Bernardo Chavira, Jose R. Rodriguez-SosaGraphical abstractClearing and immunofluorescence of whole samples from murine testes for their subsequent three-dimensional reconstruction by confocal microscopy. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 11, 2020 Category: Biology Source Type: research

In situ 3D visualization of biomineralization matrix proteins
Publication date: Available online 9 January 2020Source: Journal of Structural BiologyAuthor(s): Oliver R.B. Thomas, Kay L. Richards, Steven Petrou, Blaine R. Roberts, Stephen E. SwearerAbstractCalcium biominerals occur in all major animal phyla, and through biomolecular control, exhibit such diverse structures as exoskeletons, shells, bones, teeth and earstones (otoliths). Determining the three-dimensional expression of key biomineral proteins, however, has proven challenging as typical protein identification methods either lose spatial resolution during dissolution of the mineral phase or are costly and limited to two-di...
Source: Journal of Structural Biology - January 9, 2020 Category: Biology Source Type: research

Outside Front Cover
Publication date: 1 January 2020Source: Journal of Structural Biology, Volume 209, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 7, 2020 Category: Biology Source Type: research

Editorial Board
Publication date: 1 January 2020Source: Journal of Structural Biology, Volume 209, Issue 1Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - January 7, 2020 Category: Biology Source Type: research

Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening
Publication date: Available online 3 January 2020Source: Journal of Structural BiologyAuthor(s): J.L. Vilas, J. Vargas, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Jimenez-Moreno, E. Garduño, P. Conesa, R. Marabini, D. Maluenda, J.M. Carazo, C.O.S. SorzanoAbstractThe analysis of structure factors in 3D cryo-EM Coulomb potential maps and their “enhancement” at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is b...
Source: Journal of Structural Biology - January 5, 2020 Category: Biology Source Type: research

Journal of Structural Biology – Paper of the Year 2019
Publication date: Available online 23 December 2019Source: Journal of Structural BiologyAuthor(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - December 24, 2019 Category: Biology Source Type: research

Inverse Folding with RNA-As-Graphs Produces a Large Pool of Candidate Sequences with Target Topologies
We present an RNA-As-Graphs (RAG) based inverse folding algorithm, RAG-IF, to design novel RNA sequences that fold onto target tree graph topologies. The algorithm can be used to enhance our recently reported computational design pipeline (Jain et. al, NAR 2018). The RAG approah reresents RNA secondary structures as tree and dual graphs, where RNA loops and helices are coarse-grained as vertices and edges, opening the usage of graph theory methods to study, predict, and design RNA structures. Our recently developed computational pipeline for design utilizes graph partitioning (RAG-3D) and atomic fragment assembly (F-RAG) t...
Source: Journal of Structural Biology - December 24, 2019 Category: Biology Source Type: research

Cryo-EM reveals an asymmetry in a novel single-ring viral chaperonin
Publication date: Available online 21 December 2019Source: Journal of Structural BiologyAuthor(s): Tatiana B. Stanishneva-Konovalova, Pavel I. Semenyuk, Lidia P. Kurochkina, Evgeny B. Pichkur, Alexander L. Vasilyev, Mikhail V. Kovalchuk, Mikhail P. Kirpichnikov, Olga S. SokolovaAbstractChaperonins are ubiquitously present protein complexes, which assist the proper folding of newly synthesized proteins and prevent aggregation of denatured proteins in an ATP-dependent manner. They are classified into group I (bacterial, mitochondrial, chloroplast chaperonins) and group II (archaeal and eukaryotic cytosolic variants). However...
Source: Journal of Structural Biology - December 21, 2019 Category: Biology Source Type: research

Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy
Publication date: Available online 19 December 2019Source: Journal of Structural BiologyAuthor(s): Feng Wang, Zanlin Yu, Miguel Betegon, Melody G. Campbell, Tural Aksel, Jianhua Zhao, Sam Li, Shawn M. Douglas, Yifan Cheng, David A. AgardAbstractCryo-EM samples prepared using traditional methods often suffer from too few particles, poor particle distribution, strongly biased orientation, or damage from the air-water interface. Here we report that functionalization of graphene oxide (GO) coated grids with amino groups concentrates samples on the grid with improved distribution and orientation. By introducing a PEG spacer, pa...
Source: Journal of Structural Biology - December 20, 2019 Category: Biology Source Type: research

Use of β3-methionine as an amino acid substrate of Escherichia coli Methionyl-tRNA synthetase
This study provides structural and biochemical bases for engineering MetRS with improved β3-Met aminoacylation capabilities. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - December 18, 2019 Category: Biology Source Type: research

Outside Front Cover
Publication date: 1 November 2019Source: Journal of Structural Biology, Volume 208, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - December 17, 2019 Category: Biology Source Type: research

Structure comparison of the chimeric AAV2.7m8 vector with parental AAV2
Publication date: Available online 16 December 2019Source: Journal of Structural BiologyAuthor(s): Antonette Bennett, Annahita Keravala, Victoria Makal, Justin Kurian, Brahim Belbellaa, Rangoli Aeran, Yu-Shan Tseng, Duncan Sousa, John Spear, Mehdi Gasmi, Mavis Agbandje-McKennaAbstractThe AAV2.7m8 vector is an engineered capsid with a 10-amino acid insertion in adeno-associated virus (AAV) surface variable region VIII (VR-VIII) resulting in the alteration of an antigenic region of AAV2 and the ability to efficiently transduce retina cells following intravitreal administration. Directed evolution and in vivo screening in the...
Source: Journal of Structural Biology - December 17, 2019 Category: Biology Source Type: research

Structural and DNA Binding Properties of Mycobacterial Integration Host Factor mIHF
Publication date: Available online 14 December 2019Source: Journal of Structural BiologyAuthor(s): Nina T. Odermatt, Moreno Lelli, Torsten Herrmann, Luciano A. Abriata, Aleksandre Japaridze, Hubert Voilquin, Rajkumar Singh, Jérémie Piton, Lyndon Emsley, Giovanni Dietler, Stewart T. ColeAbstractIn bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted to Actinobacteria and essential for survival of the human pathog...
Source: Journal of Structural Biology - December 14, 2019 Category: Biology Source Type: research

Quantification of sheet nacre morphogenesis using X-ray nanotomography and deep learning
Publication date: Available online 6 December 2019Source: Journal of Structural BiologyAuthor(s): Maksim Beliaev, Dana Zöllner, Alexandra Pacureanu, Paul Zaslansky, Luca Bertinetti, Igor ZlotnikovAbstractHigh-resolution three-dimensional imaging is key to our understanding of biological tissue formation and function. Recent developments in synchrotron-based X-Ray tomography techniques provide unprecedented morphological information on relatively large sample volumes with a spatial resolution better than 50 nm. However, the analysis of the generated data, in particular image segmentation – separation into structu...
Source: Journal of Structural Biology - December 7, 2019 Category: Biology Source Type: research

Coral Acid Rich Protein Selects Vaterite Polymorph in vitro
Publication date: Available online 4 December 2019Source: Journal of Structural BiologyAuthor(s): Ra'anan Laipnik, Veronica Bissi, Chang-Yu Sun, Giuseppe Falini, P.U.P.A. Gilbert, Tali MassAbstractCorals and other biomineralizing organisms use proteins and other molecules to form different crystalline polymorphs and biomineral structures. In corals, it’s been suggested that proteins such as Coral Acid Rich Proteins (CARPs) play a major role in the polymorph selection of their calcium carbonate (CaCO3) aragonite exoskeleton. To date, four CARPs (1-4) have been characterized: each with a different amino acid compositio...
Source: Journal of Structural Biology - December 5, 2019 Category: Biology Source Type: research

Higher order assembling of the mycobacterial polar growth factor DivIVA/Wag31
We report biophysical characterizations of filaments formed by mycobacterial Wag31 using circular dichroism, atomic force microscopy and small angle solution X-ray scattering. Atomic force microscopic images of the wild-type, a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of Wag31 show mostly linear filament formation with occasional curving, kinking and apparent branching. Solution X-ray scattering data indicates that the phospho-mimetic forms of the Wag31 polymers are on average more compact than their phospho-ablative counterparts, which is likely due to the extent of bending/branching. Observed structural ...
Source: Journal of Structural Biology - November 26, 2019 Category: Biology Source Type: research

The paradoxical effects of progesterone on the eggshell quality of laying hens
This study demonstrates the effects of progesterone on eggshell quality and ultrastructure by injecting progesterone into laying hens 2 and 5 h post-oviposition, respectively. Progesterone injected 2 h post-oviposition (P4-2 h) improved eggshell quality with a significant decrease (P
Source: Journal of Structural Biology - November 26, 2019 Category: Biology Source Type: research

Do sequence neighbours of intrinsically disordered regions promote structural flexibility in intrinsically disordered proteins?
Publication date: Available online 20 November 2019Source: Journal of Structural BiologyAuthor(s): Sushmita Basu, Ranjit Prasad BahadurAbstractIntrinsically disordered proteins (IDPs) are crucial players in various cellular activities. Several experimental and computational analyses have been conducted to study structural pliability and functional potential of IDPs. In spite of active research in past few decades, what induces structural disorder in IDPs and how is still elusive. Many studies testify that sequential and spatial neighbours often play important roles in determining structural and functional behaviour of prot...
Source: Journal of Structural Biology - November 21, 2019 Category: Biology Source Type: research

Outside Front Cover
Publication date: 1 December 2019Source: Journal of Structural Biology, Volume 208, Issue 3Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 21, 2019 Category: Biology Source Type: research

Publisher's Note
Publication date: 1 December 2019Source: Journal of Structural Biology, Volume 208, Issue 3Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 21, 2019 Category: Biology Source Type: research

Editorial Board
Publication date: 1 December 2019Source: Journal of Structural Biology, Volume 208, Issue 3Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 21, 2019 Category: Biology Source Type: research

Structural features of split and unsplit βαβ-units
In this study, 1064 nonhomologous “unsplit”, “one-strand split” and “two-strand split” right-handed βαβ-units having standard α-helices and loops up to seven residues in length have been analyzed. It was found that the α-helices in these kinds of βαβ-units have different distributions of the hydrophobic and hydrophilic amino acid residues along the chain. In the unsplit βαβ-units, most α-helices have hydrophobic residues in positions N4-N7-N8-N11 or N6-N7-N10, where N1 is the first N-terminal residue. In the one-strand spl...
Source: Journal of Structural Biology - November 19, 2019 Category: Biology Source Type: research

Crystal structure of TbEsa1 presumed Tudor domain from Trypanosoma brucei
Publication date: Available online 17 November 2019Source: Journal of Structural BiologyAuthor(s): Jie Gao, Kaiqin Ye, Yating Diwu, Chao Xu, Xuecheng Zhang, Shanhui Liao, Xiaoming TuAbstractThe essential SAS2-related acetyltransferase 1 (Esa1), as a acetyltransferase of MYST family, is indispensable for the cell cycle and transcriptional regulation. The Tudor domain consists of 60 amino acids and belongs to the Royal family, which serves as a module interacting with methylated histone and/or DNA. Although Tudor domain has been widely studied in higher eukaryotes, its structure and function remain unclear in Trypanosoma bru...
Source: Journal of Structural Biology - November 18, 2019 Category: Biology Source Type: research

Segmentation by Classification: A Novel and Reliable Approach for Semi-Automatic Selection of HIV/SIV Envelope Spikes
We describe a semiautomated approach to segment Env spikes from the membrane envelope of Simian Immunodeficiency Virus visualized by cryoelectron tomography of frozen-hydrated specimens. Multivariate data analysis is applied to a large set of overlapping subvolumes extracted semiautomatically from the viral envelope and does not utilize a template of the target structure. The major manual step used in the method involves determination of six points that define an ellipsoid approximating the virion shape. The approach is robust to departures of the actual virion from this starting ellipsoid. A point cage of sufficient densi...
Source: Journal of Structural Biology - November 15, 2019 Category: Biology Source Type: research

Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex
We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to an exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to a G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3′-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5′-end G•G•G•G and G•G•A•T tetrads, ...
Source: Journal of Structural Biology - November 13, 2019 Category: Biology Source Type: research

Structural and functional investigation of AerF, a NADPH-dependent alkenal double bond reductase participating in the biosynthesis of Choi moiety of aeruginosin
In this study, functional and mechanistic analyses of AerF from Microcystis aeruginosa were performed. Observation of enzymatic assay demonstrates that AerF is a NADPH-dependent alkenal double bond reductase that catalyzes the reduction of dihydro-4-hydroxyphenylpyruvate (H2HPP) to generate tetrahydro-4-hydroxyphenylpyruvate (H4HPP), which is the third step of the biosynthetic pathway from prephenate to Choi. Comparative structural analysis indicates that ligand binding-induced conformational change of AerF is different from that of the other SDR superfamily reductase using H2HPP as a substrate. Analyses of NADPH and subst...
Source: Journal of Structural Biology - November 12, 2019 Category: Biology Source Type: research

Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections
Publication date: Available online 11 November 2019Source: Journal of Structural BiologyAuthor(s): Eric J. Verbeke, Yi Zhou, Andrew P. Horton, Anna L. Mallam, David W. Taylor, Edward M. MarcotteAbstractSingle particle analysis for structure determination in cryo-electron microscopy is traditionally applied to samples purified to near homogeneity as current reconstruction algorithms are not designed to handle heterogeneous mixtures of structures from many distinct macromolecular complexes. We extend on long established methods and demonstrate that relating two-dimensional projection images by their common lines in a graphic...
Source: Journal of Structural Biology - November 12, 2019 Category: Biology Source Type: research

Corrigendum to “Fourier-space TEM reconstructions with symmetry adapted functions for all rotational point groups” [J. Struct. Biol. 182 (2013) 87–92]
Publication date: Available online 8 November 2019Source: Journal of Structural BiologyAuthor(s): Stefano Trapani, Jorge Navaza (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - November 10, 2019 Category: Biology Source Type: research

Conformational properties of L-fucose and the tetrasaccharide building block of the sulfated L-fucan from Lytechinus variegatus
Publication date: Available online 4 November 2019Source: Journal of Structural BiologyAuthor(s): Francisco F. Bezerra, William P. Vignovich, AyoOluwa O. Aderibigbe, Hao Liu, Joshua S. Sharp, Robert J. Doerksen, Vitor H. PominAbstractAlthough the 3D structure of carbohydrates is known to contribute to their biological roles, conformational studies of sugars are challenging because their chains are flexible in solution and consequently the number of 3D structural restraints is limited. Here, we investigate the conformational properties of the tetrasaccharide building block of the Lytechinus variegatus sulfated fucan compose...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research

Tidy up cryo-EM sample grids with 3D printed tools
Publication date: Available online 4 November 2019Source: Journal of Structural BiologyAuthor(s): Tasuku Hamaguchi, Koji YonekuraAbstractCryo-EM technology has developed to the point of high-throughput structure determination of biological macromolecules embedded in vitreous ice. Nonetheless, challenging targets need extensive sample screening, often of many cryo-EM sample grids prepared under various conditions. We have designed and made tools for manipulating sample grids in storage cases. These tools are made of a plastic fiber using a wide-use 3D printer, a fused deposition modeling type, and polished under acetone gas...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research

Lepidosaur ß-Keratin Chains With Four 34-Residue Repeats: Modelling Reveals A Potential Filament-Crosslinking Role
Publication date: Available online 5 November 2019Source: Journal of Structural BiologyAuthor(s): R.D. Bruce Fraser, David A.D. ParryAbstractß-keratin chains contain a characteristic and homologous 34-residue sequence, which is believed to adopt a twisted ß-sheet conformation that assembles in an antiparallel manner with a similar sheet in a second chain to form a ß-sandwich. These sandwiches are, in turn, related to one another by a left-handed four-fold screw axis to generate a helical structure that forms the core of the 3.4 nm diameter filaments observed by electron microscopy and deduced from X-ray f...
Source: Journal of Structural Biology - November 6, 2019 Category: Biology Source Type: research

Identification of a pH Sensor in Influenza Hemagglutinin using X-ray Crystallography
Publication date: Available online 2 November 2019Source: Journal of Structural BiologyAuthor(s): Aleksandar Antanasijevic, Matthew A. Durst, Arnon Lavie, Michael CaffreyAbstractHemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in ...
Source: Journal of Structural Biology - November 3, 2019 Category: Biology Source Type: research

How the central domain of dystrophin acts to bridge F-actin to sarcolemmal lipids
Publication date: Available online 2 November 2019Source: Journal of Structural BiologyAuthor(s): Dominique Mias-Lucquin, Raphael Dos Santos Morais, Angélique Chéron, Mélanie Lagarrigue, Steve J Winder, Thomas Chenuel, Javier Pérez, Marie-Sousai Appavou, Anne Martel, Guillaume Alviset, Elisabeth Le Rumeur, Sophie Combet, Jean-François Hubert, Olivier DelalandeAbstractDystrophin is a large intracellular protein that prevents sarcolemmal ruptures by providing a mechanical link between the intracellular actin cytoskeleton and the transmembrane dystroglycan complex. Dystrophin deficiency lead...
Source: Journal of Structural Biology - November 3, 2019 Category: Biology Source Type: research

Asparagine-84, a regulatory allosteric site residue, helps maintain the quaternary structure of Campylobacter jejuni dihydrodipicolinate synthase
Publication date: Available online 31 October 2019Source: Journal of Structural BiologyAuthor(s): Mohadeseh Majdi Yazdi, Sagar Saran, Tyler Mrozowich, Cheyanne Lehnert, Trushar R. Patel, David A.R. Sanders, David R.J. PalmerAbstractDihydrodipicolinate synthase (DHDPS) from Campylobacter jejuni is a natively homotetrameric enzyme that catalyzes the first unique reaction of (S)-lysine biosynthesis and is feedback-regulated by lysine through binding to an allosteric site. High-resolution structures of the DHDPS-lysine complex have revealed significant insights into the binding events. One key asparagine residue, N84, makes hy...
Source: Journal of Structural Biology - October 31, 2019 Category: Biology Source Type: research

Dimerization of long Hibernation Promoting Factor from Staphylococcus aureus: structural analysis and biochemical characterization
In this study, we solved the crystal structure of CTDSaHPF at 1.6 Å resolution and obtained a precise arrangement of the dimer interface. Residues Phe160, Val162, Thr171, Ile173, Tyr175, Ile185 andThr187 in the dimer interface of SaHPF protein were mutated and the effects were analyzed for the formation of 100S disomes of ribosomes isolated from S. aureus. It was shown that substitution of any of single residues Phe160, Val162, Ile173, Tyr175 and Ile185 in the SaHPF homodimer interface abolished the ribosome dimerization in vitro.Graphical abstract (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 26, 2019 Category: Biology Source Type: research

Outside Front Cover - Journal name, Cover image, Volume issue details, ISSN, Cover Date, Elsevier Logo and Society Logo if required
Publication date: 1 November 2019Source: Journal of Structural Biology, Volume 208, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 23, 2019 Category: Biology Source Type: research

Editorial Board
Publication date: 1 November 2019Source: Journal of Structural Biology, Volume 208, Issue 2Author(s): (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 23, 2019 Category: Biology Source Type: research

Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain
Publication date: Available online 16 October 2019Source: Journal of Structural BiologyAuthor(s): Salomé Llabrés, Maxim I Tsenkov, Stuart A MacGowan, Geoffrey J Barton, Ulrich ZachariaeAbstractTetratricopeptide repeat (TPR) proteins belong to the class of α-solenoid proteins, in which repetitive units of α-helical hairpin motifs stack to form superhelical, often highly flexible structures. TPR domains occur in a wide variety of proteins, and perform key functional roles including protein folding, protein trafficking, cell cycle control and post-translational modification. Here, we look at the TPR ...
Source: Journal of Structural Biology - October 19, 2019 Category: Biology Source Type: research

Mineralized scale patterns on the cell periphery of the chrysophyte Mallomonas determined by comparative 3D Cryo-FIB SEM data processing
In this study, the scale case of the photosynthetic synurophyte Mallomonas was preserved in aqueous suspension using high-pressure freezing (HPF). From this specimen, a three-dimensional (3D) data set spanning a volume of about 25.6μm × 19.2μm × 4.2μm with a voxel size of 12.5nm × 12.5nm × 25.0nm was collected by Cryo-FIB SEM in 3 hours and 24 minutes. SEM imaging using In-lens SE detection allowed to clearly differentiate between mineralized, curved scales of less than 0.2μm thickness and organic cellular ultrastructure or vitrified ice. The three-dimensional spatial orientations and sh...
Source: Journal of Structural Biology - October 14, 2019 Category: Biology Source Type: research

Lateral A11 type tetramerization in lamins
Publication date: Available online 11 October 2019Source: Journal of Structural BiologyAuthor(s): Anastasia V. Lilina, Anastasia A. Chernyatina, Dmytro Guzenko, Sergei V. StrelkovAbstractThe assembly of intermediate filaments (IFs) including nuclear lamins is driven by specific interactions of the elementary coiled-coil dimers in both lateral and longitudinal direction. The assembly mode A11 is dependent on lateral tetramerization of the second coiled-coil segment (coil1b) in antiparallel fashion. Recent cryo-electron microscopy studies pointed to 3.5 nm lamin filaments built from two antiparallel threads of longitudinally...
Source: Journal of Structural Biology - October 13, 2019 Category: Biology Source Type: research

A microtubule RELION-based pipeline for cryo-EM image processing
Publication date: Available online 11 October 2019Source: Journal of Structural BiologyAuthor(s): Alexander D. Cook, Szymon W. Manka, Su Wang, Carolyn A. Moores, Joseph AthertonAbstractMicrotubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views o...
Source: Journal of Structural Biology - October 11, 2019 Category: Biology Source Type: research

High-resolution structures of annexin A5 in a two-dimensional array
This study provides molecular insight into how annexins modulate the physical properties of cell membranes as a function of Ca2+ concentration and the phospholipid composition of the membrane. (Source: Journal of Structural Biology)
Source: Journal of Structural Biology - October 10, 2019 Category: Biology Source Type: research

Modeling membrane proteins: the importance of cysteine amino-acids
Publication date: Available online 5 October 2019Source: Journal of Structural BiologyAuthor(s): Evgeni Grazhdankin, Michal Stepniewski, Henri XhaardAbstractComputational modeling of membrane proteins is critical to understand biochemical systems and to support chemical biology. In this work, we use a dataset of 448 non-redundant membrane protein chains to expose a “rule” that governs membrane protein structure: free cysteine thiols are not found accessible to oxidative compartments such as the extracellular space, but are rather involved in disulphide bridges. Taking as examples the 1018 three-dimensional mode...
Source: Journal of Structural Biology - October 7, 2019 Category: Biology Source Type: research

Recognition of different base tetrads by RHAU: X-ray crystal structure of the G4 recognition motif bound to the 3’-end tetrad of a DNA G-quadruplex
We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to the exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to the G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3'-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5’-end G•G•G•G and G•G•A•T tetrads, our c...
Source: Journal of Structural Biology - October 4, 2019 Category: Biology Source Type: research